Source: staden-io-lib Version: 1.14.14+dfsg-1 Severity: serious Justification: FTBFS Tags: bookworm sid ftbfs User: lu...@debian.org Usertags: ftbfs-20221023 ftbfs-bookworm
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > make[3]: Entering directory '/<<PKGBUILDDIR>>/tests' > PASS: srf2fasta.test > PASS: srf2fastq.test > PASS: srf_info.test > Reading archive ./data/both.srf. > PASS: srf_filter.test > NB: The next line is expected to be an error message > Malformed or missing index hash. Consider running srf_index_hash > Nbuckets = 16 > Nused = 20 > Avg chain = 1.250000 > Chain var.= 0.812500 > %age full = 81.250000 > max len = 3 > Chain 0 = 3 > Chain 1 = 8 > Chain 2 = 3 > Chain 3 = 2 > PASS: srf_index.test > Loading ce.fa > Generating ce#sorted.sam > Generating ce#unsorted.sam > === testing ./data/c1#bounds.sam === > ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam > ../progs/scramble -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ../progs/scramble -O bam test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.bam > ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -e -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -E -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -x -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam > ./compare_sam.pl --unknownrg ./data/c1#bounds.sam > test.out/c1#bounds.full.bam.sam > > === testing ./data/c1#clip.sam === > ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam > ../progs/scramble -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ../progs/scramble -O bam test.out/c1#clip.full.cram > > test.out/c1#clip.full.bam > ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -e -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -E -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -x -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam > > === testing ./data/c1#pad1.sam === > ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam > ../progs/scramble -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ../progs/scramble -O bam test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.bam > ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam > > === testing ./data/c1#pad2.sam === > ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam > ../progs/scramble -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ../progs/scramble -O bam test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.bam > ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam > > === testing ./data/c1#pad3.sam === > ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam > ../progs/scramble -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ../progs/scramble -O bam test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.bam > ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -e -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -E -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -x -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam > > === testing ./data/ce#1.sam === > ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#1.bam test.out/ce#1.full.cram > ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ../progs/scramble -O bam test.out/ce#1.full.cram > test.out/ce#1.full.bam > ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam > > === testing ./data/ce#2.sam === > ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#2.bam test.out/ce#2.full.cram > ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ../progs/scramble -O bam test.out/ce#2.full.cram > test.out/ce#2.full.bam > ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam > > === testing ./data/ce#5.sam === > ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#5.bam test.out/ce#5.full.cram > ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ../progs/scramble -O bam test.out/ce#5.full.cram > test.out/ce#5.full.bam > ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam > > === testing ./data/ce#5b.sam === > ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ../progs/scramble -O bam test.out/ce#5b.full.cram > test.out/ce#5b.full.bam > ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam > > === testing ./data/ce#large_seq.sam === > ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ../progs/scramble -O bam test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.bam > ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam > test.out/ce#large_seq.full.bam.sam > > === testing ./data/ce#sorted.sam === > ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ../progs/scramble -O bam test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.bam > ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#sorted.sam > test.out/ce#sorted.full.bam.sam > > === testing ./data/ce#tag_depadded.sam === > ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ../progs/scramble -O bam test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.bam > ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam > test.out/ce#tag_depadded.full.bam.sam > > === testing ./data/ce#tag_padded.sam === > ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ../progs/scramble -O bam test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.bam > ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam > test.out/ce#tag_padded.full.bam.sam > > === testing ./data/ce#unmap.sam === > ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ../progs/scramble -O bam test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.bam > ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap.sam > test.out/ce#unmap.full.bam.sam > > === testing ./data/ce#unmap1.sam === > ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ../progs/scramble -O bam test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.bam > ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam > test.out/ce#unmap1.full.bam.sam > > === testing ./data/ce#unmap2.sam === > ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ../progs/scramble -O bam test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.bam > ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -e -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -E -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam > test.out/ce#unmap2.full.bam.sam > > === testing ./data/ce#unsorted.sam === > ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam > ../progs/scramble -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ../progs/scramble -O bam test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.bam > ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam > test.out/ce#unsorted.full.bam.sam > ../progs/scramble -x -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam > test.out/ce#unsorted.full.bam.sam > > === testing ./data/tag_aux#aux.sam === > ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam > ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ../progs/scramble -O bam test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.bam > ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam > test.out/tag_aux#aux.full.bam.sam > > === testing ./data/tag_aux#special.sam === > ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam > ../progs/scramble -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ../progs/scramble -O bam test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.bam > ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > ../progs/scramble test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam > test.out/tag_aux#special.full.bam.sam > > === testing ./data/tag_aux#values1.bam === > ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam > ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ../progs/scramble -O bam test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.bam > ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam > test.out/tag_aux#values1.full.bam.sam > > === testing ./data/tag_aux#values2.bam === > ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam > ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ../progs/scramble -O bam test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.bam > ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam > test.out/tag_aux#values2.full.bam.sam > > === testing ./data/tag_aux#values4.bam === > ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam > ../progs/scramble -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ../progs/scramble -O bam test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.bam > ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam > test.out/tag_aux#values4.full.bam.sam > > === testing ./data/xx#MD.sam === > ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ../progs/scramble -O bam test.out/xx#MD.full.cram > test.out/xx#MD.full.bam > ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam > > === testing ./data/xx#MD2.sam === > ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ../progs/scramble -O bam test.out/xx#MD2.full.cram > > test.out/xx#MD2.full.bam > ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam > > === testing ./data/xx#blank.sam === > ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ../progs/scramble -O bam test.out/xx#blank.full.cram > > test.out/xx#blank.full.bam > ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam > ./compare_sam.pl --unknownrg ./data/xx#blank.sam > test.out/xx#blank.full.bam.sam > > === testing ./data/xx#large_aux.sam === > ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ../progs/scramble -O bam test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.bam > ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam > test.out/xx#large_aux.full.bam.sam > > === testing ./data/xx#large_aux2.sam === > ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ../progs/scramble -O bam test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.bam > ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam > test.out/xx#large_aux2.full.bam.sam > > === testing ./data/xx#minimal.sam === > ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ../progs/scramble -O bam test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.bam > ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --unknownrg ./data/xx#minimal.sam > test.out/xx#minimal.full.bam.sam > > === testing ./data/xx#pair.sam === > ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ../progs/scramble -O bam test.out/xx#pair.full.cram > > test.out/xx#pair.full.bam > ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam > > === testing ./data/xx#repeated.sam === > ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ../progs/scramble -O bam test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.bam > ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --unknownrg ./data/xx#repeated.sam > test.out/xx#repeated.full.bam.sam > > === testing ./data/xx#rg.sam === > ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ../progs/scramble -O bam test.out/xx#rg.full.cram > test.out/xx#rg.full.bam > ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam > > === testing ./data/xx#triplet.sam === > ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ../progs/scramble -O bam test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.bam > ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -e -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -E -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --unknownrg ./data/xx#triplet.sam > test.out/xx#triplet.full.bam.sam > > === testing ./data/xx#unsorted.sam === > ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam > ../progs/scramble -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ../progs/scramble -O bam test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.bam > ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam > test.out/xx#unsorted.full.bam.sam > ../progs/scramble -x -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam > test.out/xx#unsorted.full.bam.sam > > PASS: scram.test > === testing ./data/c1#bounds.sam === > ../progs/scramble ./data/c1#bounds.sam test.out/c1#bounds.bam > ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble test.out/c1#bounds.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ../progs/scramble -V3.0 -O bam test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.bam > ../progs/scramble test.out/c1#bounds.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble test.out/c1#bounds.full.cram > test.out/c1#bounds.full.sam > ./compare_sam.pl --unknownrg ./data/c1#bounds.sam > test.out/c1#bounds.full.bam.sam > > === testing ./data/c1#clip.sam === > ../progs/scramble ./data/c1#clip.sam test.out/c1#clip.bam > ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble test.out/c1#clip.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ../progs/scramble -V3.0 -O bam test.out/c1#clip.full.cram > > test.out/c1#clip.full.bam > ../progs/scramble test.out/c1#clip.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -m test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam > > === testing ./data/c1#pad1.sam === > ../progs/scramble ./data/c1#pad1.sam test.out/c1#pad1.bam > ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble test.out/c1#pad1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ../progs/scramble -V3.0 -O bam test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.bam > ../progs/scramble test.out/c1#pad1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -m test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam > > === testing ./data/c1#pad2.sam === > ../progs/scramble ./data/c1#pad2.sam test.out/c1#pad2.bam > ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble test.out/c1#pad2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ../progs/scramble -V3.0 -O bam test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.bam > ../progs/scramble test.out/c1#pad2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -m test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam > > === testing ./data/c1#pad3.sam === > ../progs/scramble ./data/c1#pad3.sam test.out/c1#pad3.bam > ../progs/scramble -V3.0 -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble test.out/c1#pad3.bam > test.out/tmp.sam > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ../progs/scramble -V3.0 -O bam test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.bam > ../progs/scramble test.out/c1#pad3.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -m test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam > > === testing ./data/ce#1.sam === > ../progs/scramble ./data/ce#1.sam test.out/ce#1.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble test.out/ce#1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#1.full.cram > > test.out/ce#1.full.bam > ../progs/scramble test.out/ce#1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam > > === testing ./data/ce#2.sam === > ../progs/scramble ./data/ce#2.sam test.out/ce#2.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble test.out/ce#2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#2.full.cram > > test.out/ce#2.full.bam > ../progs/scramble test.out/ce#2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam > > === testing ./data/ce#5.sam === > ../progs/scramble ./data/ce#5.sam test.out/ce#5.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble test.out/ce#5.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#5.full.cram > > test.out/ce#5.full.bam > ../progs/scramble test.out/ce#5.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam > > === testing ./data/ce#5b.sam === > ../progs/scramble ./data/ce#5b.sam test.out/ce#5b.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble test.out/ce#5b.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#5b.full.cram > > test.out/ce#5b.full.bam > ../progs/scramble test.out/ce#5b.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam > > === testing ./data/ce#large_seq.sam === > ../progs/scramble ./data/ce#large_seq.sam test.out/ce#large_seq.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble test.out/ce#large_seq.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.bam > ../progs/scramble test.out/ce#large_seq.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam > test.out/ce#large_seq.full.bam.sam > > === testing ./data/ce#sorted.sam === > ../progs/scramble ./data/ce#sorted.sam test.out/ce#sorted.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble test.out/ce#sorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.bam > ../progs/scramble test.out/ce#sorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble test.out/ce#sorted.full.cram > test.out/ce#sorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#sorted.sam > test.out/ce#sorted.full.bam.sam > > === testing ./data/ce#tag_depadded.sam === > ../progs/scramble ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble test.out/ce#tag_depadded.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.bam > ../progs/scramble test.out/ce#tag_depadded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam > test.out/ce#tag_depadded.full.bam.sam > > === testing ./data/ce#tag_padded.sam === > ../progs/scramble ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble test.out/ce#tag_padded.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.bam > ../progs/scramble test.out/ce#tag_padded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam > test.out/ce#tag_padded.full.bam.sam > > === testing ./data/ce#unmap.sam === > ../progs/scramble ./data/ce#unmap.sam test.out/ce#unmap.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble test.out/ce#unmap.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.bam > ../progs/scramble test.out/ce#unmap.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble test.out/ce#unmap.full.cram > test.out/ce#unmap.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap.sam > test.out/ce#unmap.full.bam.sam > > === testing ./data/ce#unmap1.sam === > ../progs/scramble ./data/ce#unmap1.sam test.out/ce#unmap1.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble test.out/ce#unmap1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.bam > ../progs/scramble test.out/ce#unmap1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble test.out/ce#unmap1.full.cram > test.out/ce#unmap1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam > test.out/ce#unmap1.full.bam.sam > > === testing ./data/ce#unmap2.sam === > ../progs/scramble ./data/ce#unmap2.sam test.out/ce#unmap2.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble test.out/ce#unmap2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.bam > ../progs/scramble test.out/ce#unmap2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble test.out/ce#unmap2.full.cram > test.out/ce#unmap2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam > test.out/ce#unmap2.full.bam.sam > > === testing ./data/ce#unsorted.sam === > ../progs/scramble ./data/ce#unsorted.sam test.out/ce#unsorted.bam > ../progs/scramble -V3.0 -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble test.out/ce#unsorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ../progs/scramble -V3.0 -O bam test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.bam > ../progs/scramble test.out/ce#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam > test.out/ce#unsorted.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam > test.out/ce#unsorted.full.bam.sam > > === testing ./data/tag_aux#aux.sam === > ../progs/scramble ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam > ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble test.out/tag_aux#aux.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ../progs/scramble -V3.0 -O bam test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.bam > ../progs/scramble test.out/tag_aux#aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam > test.out/tag_aux#aux.full.bam.sam > > === testing ./data/tag_aux#special.sam === > ../progs/scramble ./data/tag_aux#special.sam test.out/tag_aux#special.bam > ../progs/scramble -V3.0 -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > ../progs/scramble test.out/tag_aux#special.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ../progs/scramble -V3.0 -O bam test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.bam > ../progs/scramble test.out/tag_aux#special.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa > test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa > test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa > test.out/tag_aux#special.bam test.out/tag_aux#special.full.cram > ../progs/scramble test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam > test.out/tag_aux#special.full.bam.sam > > === testing ./data/tag_aux#values1.bam === > ../progs/scramble ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam > ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble ./data/tag_aux#values1.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ../progs/scramble -V3.0 -O bam test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.bam > ../progs/scramble test.out/tag_aux#values1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam > test.out/tag_aux#values1.full.bam.sam > > === testing ./data/tag_aux#values2.bam === > ../progs/scramble ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam > ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble ./data/tag_aux#values2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ../progs/scramble -V3.0 -O bam test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.bam > ../progs/scramble test.out/tag_aux#values2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam > test.out/tag_aux#values2.full.bam.sam > > === testing ./data/tag_aux#values4.bam === > ../progs/scramble ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam > ../progs/scramble -V3.0 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble ./data/tag_aux#values4.bam > test.out/tmp.sam > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ../progs/scramble -V3.0 -O bam test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.bam > ../progs/scramble test.out/tag_aux#values4.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam > test.out/tag_aux#values4.full.bam.sam > > === testing ./data/xx#MD.sam === > ../progs/scramble ./data/xx#MD.sam test.out/xx#MD.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble test.out/xx#MD.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#MD.full.cram > > test.out/xx#MD.full.bam > ../progs/scramble test.out/xx#MD.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam > > === testing ./data/xx#MD2.sam === > ../progs/scramble ./data/xx#MD2.sam test.out/xx#MD2.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble test.out/xx#MD2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#MD2.full.cram > > test.out/xx#MD2.full.bam > ../progs/scramble test.out/xx#MD2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam > > === testing ./data/xx#blank.sam === > ../progs/scramble ./data/xx#blank.sam test.out/xx#blank.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble test.out/xx#blank.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#blank.full.cram > > test.out/xx#blank.full.bam > ../progs/scramble test.out/xx#blank.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble test.out/xx#blank.full.cram > test.out/xx#blank.full.sam > ./compare_sam.pl --unknownrg ./data/xx#blank.sam > test.out/xx#blank.full.bam.sam > > === testing ./data/xx#large_aux.sam === > ../progs/scramble ./data/xx#large_aux.sam test.out/xx#large_aux.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble test.out/xx#large_aux.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.bam > ../progs/scramble test.out/xx#large_aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam > test.out/xx#large_aux.full.bam.sam > > === testing ./data/xx#large_aux2.sam === > ../progs/scramble ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble test.out/xx#large_aux2.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.bam > ../progs/scramble test.out/xx#large_aux2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam > test.out/xx#large_aux2.full.bam.sam > > === testing ./data/xx#minimal.sam === > ../progs/scramble ./data/xx#minimal.sam test.out/xx#minimal.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble test.out/xx#minimal.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.bam > ../progs/scramble test.out/xx#minimal.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --unknownrg ./data/xx#minimal.sam > test.out/xx#minimal.full.bam.sam > > === testing ./data/xx#pair.sam === > ../progs/scramble ./data/xx#pair.sam test.out/xx#pair.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble test.out/xx#pair.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#pair.full.cram > > test.out/xx#pair.full.bam > ../progs/scramble test.out/xx#pair.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -m test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam > > === testing ./data/xx#repeated.sam === > ../progs/scramble ./data/xx#repeated.sam test.out/xx#repeated.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble test.out/xx#repeated.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.bam > ../progs/scramble test.out/xx#repeated.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --unknownrg ./data/xx#repeated.sam > test.out/xx#repeated.full.bam.sam > > === testing ./data/xx#rg.sam === > ../progs/scramble ./data/xx#rg.sam test.out/xx#rg.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble test.out/xx#rg.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#rg.full.cram > > test.out/xx#rg.full.bam > ../progs/scramble test.out/xx#rg.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam > > === testing ./data/xx#triplet.sam === > ../progs/scramble ./data/xx#triplet.sam test.out/xx#triplet.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble test.out/xx#triplet.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.bam > ../progs/scramble test.out/xx#triplet.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -V3.0 -e -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -V3.0 -E -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --unknownrg ./data/xx#triplet.sam > test.out/xx#triplet.full.bam.sam > > === testing ./data/xx#unsorted.sam === > ../progs/scramble ./data/xx#unsorted.sam test.out/xx#unsorted.bam > ../progs/scramble -V3.0 -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.bam > test.out/tmp.sam > ../progs/scramble -m test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ../progs/scramble -V3.0 -O bam test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.bam > ../progs/scramble test.out/xx#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam > test.out/xx#unsorted.full.bam.sam > ../progs/scramble -V3.0 -x -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam > test.out/xx#unsorted.full.bam.sam > > === testing ./data/c1#bounds.sam === > ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam > ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -t4 test.out/c1#bounds.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ../progs/scramble -t4 -O bam test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.bam > ../progs/scramble -t4 test.out/c1#bounds.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -t4 -m test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#bounds.full.sam > test.out/c1#bounds.full.bam.sam > ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > ../progs/scramble -t4 test.out/c1#bounds.full.cram > > test.out/c1#bounds.full.sam > ./compare_sam.pl --unknownrg ./data/c1#bounds.sam > test.out/c1#bounds.full.bam.sam > > === testing ./data/c1#clip.sam === > ../progs/scramble -t4 ./data/c1#clip.sam test.out/c1#clip.bam > ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -t4 test.out/c1#clip.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/c1#clip.full.cram > > test.out/c1#clip.full.sam > ../progs/scramble -t4 -O bam test.out/c1#clip.full.cram > > test.out/c1#clip.full.bam > ../progs/scramble -t4 test.out/c1#clip.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -t4 -m test.out/c1#clip.full.cram > > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -t4 -m test.out/c1#clip.full.cram > > test.out/c1#clip.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#clip.full.sam > test.out/c1#clip.full.bam.sam > ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#clip.bam > test.out/c1#clip.full.cram > ../progs/scramble -t4 test.out/c1#clip.full.cram > test.out/c1#clip.full.sam > ./compare_sam.pl --unknownrg ./data/c1#clip.sam test.out/c1#clip.full.bam.sam > > === testing ./data/c1#pad1.sam === > ../progs/scramble -t4 ./data/c1#pad1.sam test.out/c1#pad1.bam > ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -t4 test.out/c1#pad1.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.sam > ../progs/scramble -t4 -O bam test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.bam > ../progs/scramble -t4 test.out/c1#pad1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -t4 -m test.out/c1#pad1.full.cram > > test.out/c1#pad1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad1.full.sam > test.out/c1#pad1.full.bam.sam > ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad1.bam > test.out/c1#pad1.full.cram > ../progs/scramble -t4 test.out/c1#pad1.full.cram > test.out/c1#pad1.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad1.sam test.out/c1#pad1.full.bam.sam > > === testing ./data/c1#pad2.sam === > ../progs/scramble -t4 ./data/c1#pad2.sam test.out/c1#pad2.bam > ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -t4 test.out/c1#pad2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.sam > ../progs/scramble -t4 -O bam test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.bam > ../progs/scramble -t4 test.out/c1#pad2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -t4 -m test.out/c1#pad2.full.cram > > test.out/c1#pad2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad2.full.sam > test.out/c1#pad2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad2.bam > test.out/c1#pad2.full.cram > ../progs/scramble -t4 test.out/c1#pad2.full.cram > test.out/c1#pad2.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad2.sam test.out/c1#pad2.full.bam.sam > > === testing ./data/c1#pad3.sam === > ../progs/scramble -t4 ./data/c1#pad3.sam test.out/c1#pad3.bam > ../progs/scramble -t4 -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -t4 test.out/c1#pad3.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.sam > ../progs/scramble -t4 -O bam test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.bam > ../progs/scramble -t4 test.out/c1#pad3.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -t4 -e -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -t4 -E -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -t4 -m test.out/c1#pad3.full.cram > > test.out/c1#pad3.full.sam > ./compare_sam.pl --partialmd --nopg test.out/c1#pad3.full.sam > test.out/c1#pad3.full.bam.sam > ../progs/scramble -t4 -x -r ./data/c1.fa test.out/c1#pad3.bam > test.out/c1#pad3.full.cram > ../progs/scramble -t4 test.out/c1#pad3.full.cram > test.out/c1#pad3.full.sam > ./compare_sam.pl --unknownrg ./data/c1#pad3.sam test.out/c1#pad3.full.bam.sam > > === testing ./data/ce#1.sam === > ../progs/scramble -t4 ./data/ce#1.sam test.out/ce#1.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -t4 test.out/ce#1.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ../progs/scramble -t4 -O bam test.out/ce#1.full.cram > > test.out/ce#1.full.bam > ../progs/scramble -t4 test.out/ce#1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -t4 -m test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#1.full.sam > test.out/ce#1.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#1.bam > test.out/ce#1.full.cram > ../progs/scramble -t4 test.out/ce#1.full.cram > test.out/ce#1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#1.sam test.out/ce#1.full.bam.sam > > === testing ./data/ce#2.sam === > ../progs/scramble -t4 ./data/ce#2.sam test.out/ce#2.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -t4 test.out/ce#2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ../progs/scramble -t4 -O bam test.out/ce#2.full.cram > > test.out/ce#2.full.bam > ../progs/scramble -t4 test.out/ce#2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -t4 -m test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#2.full.sam > test.out/ce#2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#2.bam > test.out/ce#2.full.cram > ../progs/scramble -t4 test.out/ce#2.full.cram > test.out/ce#2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#2.sam test.out/ce#2.full.bam.sam > > === testing ./data/ce#5.sam === > ../progs/scramble -t4 ./data/ce#5.sam test.out/ce#5.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -t4 test.out/ce#5.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ../progs/scramble -t4 -O bam test.out/ce#5.full.cram > > test.out/ce#5.full.bam > ../progs/scramble -t4 test.out/ce#5.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -t4 -m test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5.full.sam > test.out/ce#5.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5.bam > test.out/ce#5.full.cram > ../progs/scramble -t4 test.out/ce#5.full.cram > test.out/ce#5.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5.sam test.out/ce#5.full.bam.sam > > === testing ./data/ce#5b.sam === > ../progs/scramble -t4 ./data/ce#5b.sam test.out/ce#5b.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -t4 test.out/ce#5b.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ../progs/scramble -t4 -O bam test.out/ce#5b.full.cram > > test.out/ce#5b.full.bam > ../progs/scramble -t4 test.out/ce#5b.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -t4 -m test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#5b.full.sam > test.out/ce#5b.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#5b.bam > test.out/ce#5b.full.cram > ../progs/scramble -t4 test.out/ce#5b.full.cram > test.out/ce#5b.full.sam > ./compare_sam.pl --unknownrg ./data/ce#5b.sam test.out/ce#5b.full.bam.sam > > === testing ./data/ce#large_seq.sam === > ../progs/scramble -t4 ./data/ce#large_seq.sam test.out/ce#large_seq.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -t4 test.out/ce#large_seq.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ../progs/scramble -t4 -O bam test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.bam > ../progs/scramble -t4 test.out/ce#large_seq.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -t4 -m test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#large_seq.full.sam > test.out/ce#large_seq.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#large_seq.bam > test.out/ce#large_seq.full.cram > ../progs/scramble -t4 test.out/ce#large_seq.full.cram > > test.out/ce#large_seq.full.sam > ./compare_sam.pl --unknownrg ./data/ce#large_seq.sam > test.out/ce#large_seq.full.bam.sam > > === testing ./data/ce#sorted.sam === > ../progs/scramble -t4 ./data/ce#sorted.sam test.out/ce#sorted.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -t4 test.out/ce#sorted.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ../progs/scramble -t4 -O bam test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.bam > ../progs/scramble -t4 test.out/ce#sorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -t4 -m test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#sorted.full.sam > test.out/ce#sorted.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#sorted.bam > test.out/ce#sorted.full.cram > ../progs/scramble -t4 test.out/ce#sorted.full.cram > > test.out/ce#sorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#sorted.sam > test.out/ce#sorted.full.bam.sam > > === testing ./data/ce#tag_depadded.sam === > ../progs/scramble -t4 ./data/ce#tag_depadded.sam test.out/ce#tag_depadded.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -t4 test.out/ce#tag_depadded.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ../progs/scramble -t4 -O bam test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.bam > ../progs/scramble -t4 test.out/ce#tag_depadded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -t4 -m test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_depadded.full.sam > test.out/ce#tag_depadded.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_depadded.bam > test.out/ce#tag_depadded.full.cram > ../progs/scramble -t4 test.out/ce#tag_depadded.full.cram > > test.out/ce#tag_depadded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_depadded.sam > test.out/ce#tag_depadded.full.bam.sam > > === testing ./data/ce#tag_padded.sam === > ../progs/scramble -t4 ./data/ce#tag_padded.sam test.out/ce#tag_padded.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -t4 test.out/ce#tag_padded.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ../progs/scramble -t4 -O bam test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.bam > ../progs/scramble -t4 test.out/ce#tag_padded.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -t4 -m test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#tag_padded.full.sam > test.out/ce#tag_padded.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#tag_padded.bam > test.out/ce#tag_padded.full.cram > ../progs/scramble -t4 test.out/ce#tag_padded.full.cram > > test.out/ce#tag_padded.full.sam > ./compare_sam.pl --unknownrg ./data/ce#tag_padded.sam > test.out/ce#tag_padded.full.bam.sam > > === testing ./data/ce#unmap.sam === > ../progs/scramble -t4 ./data/ce#unmap.sam test.out/ce#unmap.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -t4 test.out/ce#unmap.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ../progs/scramble -t4 -O bam test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.bam > ../progs/scramble -t4 test.out/ce#unmap.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -t4 -m test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap.full.sam > test.out/ce#unmap.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap.bam > test.out/ce#unmap.full.cram > ../progs/scramble -t4 test.out/ce#unmap.full.cram > > test.out/ce#unmap.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap.sam > test.out/ce#unmap.full.bam.sam > > === testing ./data/ce#unmap1.sam === > ../progs/scramble -t4 ./data/ce#unmap1.sam test.out/ce#unmap1.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble -t4 test.out/ce#unmap1.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ../progs/scramble -t4 -O bam test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.bam > ../progs/scramble -t4 test.out/ce#unmap1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap1.full.sam > test.out/ce#unmap1.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap1.bam > test.out/ce#unmap1.full.cram > ../progs/scramble -t4 test.out/ce#unmap1.full.cram > > test.out/ce#unmap1.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap1.sam > test.out/ce#unmap1.full.bam.sam > > === testing ./data/ce#unmap2.sam === > ../progs/scramble -t4 ./data/ce#unmap2.sam test.out/ce#unmap2.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble -t4 test.out/ce#unmap2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ../progs/scramble -t4 -O bam test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.bam > ../progs/scramble -t4 test.out/ce#unmap2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unmap2.full.sam > test.out/ce#unmap2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unmap2.bam > test.out/ce#unmap2.full.cram > ../progs/scramble -t4 test.out/ce#unmap2.full.cram > > test.out/ce#unmap2.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unmap2.sam > test.out/ce#unmap2.full.bam.sam > > === testing ./data/ce#unsorted.sam === > ../progs/scramble -t4 ./data/ce#unsorted.sam test.out/ce#unsorted.bam > ../progs/scramble -t4 -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble -t4 test.out/ce#unsorted.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ../progs/scramble -t4 -O bam test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.bam > ../progs/scramble -t4 test.out/ce#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/ce#unsorted.full.sam > test.out/ce#unsorted.full.bam.sam > ../progs/scramble -t4 -x -r ./data/ce.fa test.out/ce#unsorted.bam > test.out/ce#unsorted.full.cram > ../progs/scramble -t4 test.out/ce#unsorted.full.cram > > test.out/ce#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/ce#unsorted.sam > test.out/ce#unsorted.full.bam.sam > > === testing ./data/tag_aux#aux.sam === > ../progs/scramble -t4 ./data/tag_aux#aux.sam test.out/tag_aux#aux.bam > ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble -t4 test.out/tag_aux#aux.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ../progs/scramble -t4 -O bam test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.bam > ../progs/scramble -t4 test.out/tag_aux#aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#aux.full.sam > test.out/tag_aux#aux.full.bam.sam > ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#aux.bam > test.out/tag_aux#aux.full.cram > ../progs/scramble -t4 test.out/tag_aux#aux.full.cram > > test.out/tag_aux#aux.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#aux.sam > test.out/tag_aux#aux.full.bam.sam > > === testing ./data/tag_aux#special.sam === > ../progs/scramble -t4 ./data/tag_aux#special.sam test.out/tag_aux#special.bam > ../progs/scramble -t4 -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > ../progs/scramble -t4 test.out/tag_aux#special.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ../progs/scramble -t4 -O bam test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.bam > ../progs/scramble -t4 test.out/tag_aux#special.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -t4 -e -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -t4 -E -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#special.full.sam > test.out/tag_aux#special.full.bam.sam > ../progs/scramble -t4 -x -r ./data/tag_aux.fa test.out/tag_aux#special.bam > test.out/tag_aux#special.full.cram > ../progs/scramble -t4 test.out/tag_aux#special.full.cram > > test.out/tag_aux#special.full.sam > ./compare_sam.pl --unknownrg ./data/tag_aux#special.sam > test.out/tag_aux#special.full.bam.sam > > === testing ./data/tag_aux#values1.bam === > ../progs/scramble -t4 ./data/tag_aux#values1.bam test.out/tag_aux#values1.sam > ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble -t4 ./data/tag_aux#values1.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ../progs/scramble -t4 -O bam test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.bam > ../progs/scramble -t4 test.out/tag_aux#values1.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values1.full.sam > test.out/tag_aux#values1.full.bam.sam > ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values1.bam > test.out/tag_aux#values1.full.cram > ../progs/scramble -t4 test.out/tag_aux#values1.full.cram > > test.out/tag_aux#values1.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values1.sam > test.out/tag_aux#values1.full.bam.sam > > === testing ./data/tag_aux#values2.bam === > ../progs/scramble -t4 ./data/tag_aux#values2.bam test.out/tag_aux#values2.sam > ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble -t4 ./data/tag_aux#values2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ../progs/scramble -t4 -O bam test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.bam > ../progs/scramble -t4 test.out/tag_aux#values2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values2.full.sam > test.out/tag_aux#values2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values2.bam > test.out/tag_aux#values2.full.cram > ../progs/scramble -t4 test.out/tag_aux#values2.full.cram > > test.out/tag_aux#values2.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values2.sam > test.out/tag_aux#values2.full.bam.sam > > === testing ./data/tag_aux#values4.bam === > ../progs/scramble -t4 ./data/tag_aux#values4.bam test.out/tag_aux#values4.sam > ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble -t4 ./data/tag_aux#values4.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ../progs/scramble -t4 -O bam test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.bam > ../progs/scramble -t4 test.out/tag_aux#values4.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -t4 -e -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded reference with non-coordinate sorted data is not supported. > Using -x for no-ref instead. > ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -t4 -E -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > Embedded consensus with non-coordinate sorted data is not supported. > ../progs/scramble -t4 -m test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --partialmd --nopg test.out/tag_aux#values4.full.sam > test.out/tag_aux#values4.full.bam.sam > ../progs/scramble -t4 -x -r ./data/tag_aux.fa ./data/tag_aux#values4.bam > test.out/tag_aux#values4.full.cram > ../progs/scramble -t4 test.out/tag_aux#values4.full.cram > > test.out/tag_aux#values4.full.sam > ./compare_sam.pl --unknownrg test.out/tag_aux#values4.sam > test.out/tag_aux#values4.full.bam.sam > > === testing ./data/xx#MD.sam === > ../progs/scramble -t4 ./data/xx#MD.sam test.out/xx#MD.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -t4 test.out/xx#MD.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ../progs/scramble -t4 -O bam test.out/xx#MD.full.cram > > test.out/xx#MD.full.bam > ../progs/scramble -t4 test.out/xx#MD.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -t4 -m test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD.full.sam > test.out/xx#MD.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD.bam > test.out/xx#MD.full.cram > ../progs/scramble -t4 test.out/xx#MD.full.cram > test.out/xx#MD.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD.sam test.out/xx#MD.full.bam.sam > > === testing ./data/xx#MD2.sam === > ../progs/scramble -t4 ./data/xx#MD2.sam test.out/xx#MD2.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -t4 test.out/xx#MD2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ../progs/scramble -t4 -O bam test.out/xx#MD2.full.cram > > test.out/xx#MD2.full.bam > ../progs/scramble -t4 test.out/xx#MD2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -t4 -m test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#MD2.full.sam > test.out/xx#MD2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#MD2.bam > test.out/xx#MD2.full.cram > ../progs/scramble -t4 test.out/xx#MD2.full.cram > test.out/xx#MD2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#MD2.sam test.out/xx#MD2.full.bam.sam > > === testing ./data/xx#blank.sam === > ../progs/scramble -t4 ./data/xx#blank.sam test.out/xx#blank.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -t4 test.out/xx#blank.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ../progs/scramble -t4 -O bam test.out/xx#blank.full.cram > > test.out/xx#blank.full.bam > ../progs/scramble -t4 test.out/xx#blank.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -t4 -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -t4 -m test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#blank.full.sam > test.out/xx#blank.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#blank.bam > test.out/xx#blank.full.cram > ../progs/scramble -t4 test.out/xx#blank.full.cram > > test.out/xx#blank.full.sam > ./compare_sam.pl --unknownrg ./data/xx#blank.sam > test.out/xx#blank.full.bam.sam > > === testing ./data/xx#large_aux.sam === > ../progs/scramble -t4 ./data/xx#large_aux.sam test.out/xx#large_aux.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -t4 test.out/xx#large_aux.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ../progs/scramble -t4 -O bam test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.bam > ../progs/scramble -t4 test.out/xx#large_aux.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -t4 -m test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux.full.sam > test.out/xx#large_aux.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux.bam > test.out/xx#large_aux.full.cram > ../progs/scramble -t4 test.out/xx#large_aux.full.cram > > test.out/xx#large_aux.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux.sam > test.out/xx#large_aux.full.bam.sam > > === testing ./data/xx#large_aux2.sam === > ../progs/scramble -t4 ./data/xx#large_aux2.sam test.out/xx#large_aux2.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -t4 test.out/xx#large_aux2.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ../progs/scramble -t4 -O bam test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.bam > ../progs/scramble -t4 test.out/xx#large_aux2.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -t4 -m test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#large_aux2.full.sam > test.out/xx#large_aux2.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#large_aux2.bam > test.out/xx#large_aux2.full.cram > ../progs/scramble -t4 test.out/xx#large_aux2.full.cram > > test.out/xx#large_aux2.full.sam > ./compare_sam.pl --unknownrg ./data/xx#large_aux2.sam > test.out/xx#large_aux2.full.bam.sam > > === testing ./data/xx#minimal.sam === > ../progs/scramble -t4 ./data/xx#minimal.sam test.out/xx#minimal.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -t4 test.out/xx#minimal.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ../progs/scramble -t4 -O bam test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.bam > ../progs/scramble -t4 test.out/xx#minimal.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -t4 -m test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#minimal.full.sam > test.out/xx#minimal.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#minimal.bam > test.out/xx#minimal.full.cram > ../progs/scramble -t4 test.out/xx#minimal.full.cram > > test.out/xx#minimal.full.sam > ./compare_sam.pl --unknownrg ./data/xx#minimal.sam > test.out/xx#minimal.full.bam.sam > > === testing ./data/xx#pair.sam === > ../progs/scramble -t4 ./data/xx#pair.sam test.out/xx#pair.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -t4 test.out/xx#pair.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#pair.full.cram > > test.out/xx#pair.full.sam > ../progs/scramble -t4 -O bam test.out/xx#pair.full.cram > > test.out/xx#pair.full.bam > ../progs/scramble -t4 test.out/xx#pair.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -t4 -m test.out/xx#pair.full.cram > > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -t4 -m test.out/xx#pair.full.cram > > test.out/xx#pair.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#pair.full.sam > test.out/xx#pair.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#pair.bam > test.out/xx#pair.full.cram > ../progs/scramble -t4 test.out/xx#pair.full.cram > test.out/xx#pair.full.sam > ./compare_sam.pl --unknownrg ./data/xx#pair.sam test.out/xx#pair.full.bam.sam > > === testing ./data/xx#repeated.sam === > ../progs/scramble -t4 ./data/xx#repeated.sam test.out/xx#repeated.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -t4 test.out/xx#repeated.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ../progs/scramble -t4 -O bam test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.bam > ../progs/scramble -t4 test.out/xx#repeated.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -t4 -m test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#repeated.full.sam > test.out/xx#repeated.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#repeated.bam > test.out/xx#repeated.full.cram > ../progs/scramble -t4 test.out/xx#repeated.full.cram > > test.out/xx#repeated.full.sam > ./compare_sam.pl --unknownrg ./data/xx#repeated.sam > test.out/xx#repeated.full.bam.sam > > === testing ./data/xx#rg.sam === > ../progs/scramble -t4 ./data/xx#rg.sam test.out/xx#rg.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -t4 test.out/xx#rg.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ../progs/scramble -t4 -O bam test.out/xx#rg.full.cram > > test.out/xx#rg.full.bam > ../progs/scramble -t4 test.out/xx#rg.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -t4 -m test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#rg.full.sam > test.out/xx#rg.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#rg.bam > test.out/xx#rg.full.cram > ../progs/scramble -t4 test.out/xx#rg.full.cram > test.out/xx#rg.full.sam > ./compare_sam.pl --unknownrg ./data/xx#rg.sam test.out/xx#rg.full.bam.sam > > === testing ./data/xx#triplet.sam === > ../progs/scramble -t4 ./data/xx#triplet.sam test.out/xx#triplet.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -t4 test.out/xx#triplet.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ../progs/scramble -t4 -O bam test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.bam > ../progs/scramble -t4 test.out/xx#triplet.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -t4 -e -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -t4 -E -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -t4 -m test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#triplet.full.sam > test.out/xx#triplet.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#triplet.bam > test.out/xx#triplet.full.cram > ../progs/scramble -t4 test.out/xx#triplet.full.cram > > test.out/xx#triplet.full.sam > ./compare_sam.pl --unknownrg ./data/xx#triplet.sam > test.out/xx#triplet.full.bam.sam > > === testing ./data/xx#unsorted.sam === > ../progs/scramble -t4 ./data/xx#unsorted.sam test.out/xx#unsorted.bam > ../progs/scramble -t4 -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble -t4 test.out/xx#unsorted.bam > test.out/tmp.sam > ../progs/scramble -t4 -m test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ../progs/scramble -t4 -O bam test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.bam > ../progs/scramble -t4 test.out/xx#unsorted.full.bam test.out/tmp.sam > ./compare_sam.pl --partialmd --nopg test.out/xx#unsorted.full.sam > test.out/xx#unsorted.full.bam.sam > ../progs/scramble -t4 -x -r ./data/xx.fa test.out/xx#unsorted.bam > test.out/xx#unsorted.full.cram > ../progs/scramble -t4 test.out/xx#unsorted.full.cram > > test.out/xx#unsorted.full.sam > ./compare_sam.pl --unknownrg ./data/xx#unsorted.sam > test.out/xx#unsorted.full.bam.sam > > PASS: scram_mt30.test > === testing ./data/c1#bounds.sam === > ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam > ../progs/scramble -t4 -V3.1 -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > > WARNING: this version of CRAM is not a recognised GA4GH standard. > Note this CRAM version is a technology demonstration only. > Future versions of Scramble may not be able to read these files. > > Segmentation fault > FAIL: scram_mt31.test > === testing ./data/c1#bounds.sam === > ../progs/scramble -t4 ./data/c1#bounds.sam test.out/c1#bounds.bam > ../progs/scramble -t4 -V4.0 -7 -r ./data/c1.fa test.out/c1#bounds.bam > test.out/c1#bounds.full.cram > > WARNING: this version of CRAM is not a recognised GA4GH standard. > Note this CRAM version is a technology demonstration only. > Future versions of Scramble may not be able to read these files. > > Segmentation fault > FAIL: scram_mt40.test > PASS: cram_io.test > === testing ./data/ce#5b_java.cram === > ../progs/scramble -t4 -r ./data/ce.fa ./data/ce#5b_java.cram > test.out/ce#5b_java.scramble.sam > ./compare_sam.pl ./data/ce#5b_java.sam test.out/ce#5b_java.scramble.sam > === testing ./data/tag_aux#aux_java.cram === > ../progs/scramble -t4 -r ./data/tag_aux.fa ./data/tag_aux#aux_java.cram > test.out/tag_aux#aux_java.scramble.sam > ./compare_sam.pl ./data/tag_aux#aux_java.sam > test.out/tag_aux#aux_java.scramble.sam > === testing ./data/xx#large_aux_java.cram === > ../progs/scramble -t4 -r ./data/xx.fa ./data/xx#large_aux_java.cram > test.out/xx#large_aux_java.scramble.sam > ./compare_sam.pl ./data/xx#large_aux_java.sam > test.out/xx#large_aux_java.scramble.sam > === testing ./data/9827_rand3.cram === > ../progs/scramble -t4 -r ./data/9827_rand3.cram ./data/9827_rand3.cram > test.out/9827_rand3.scramble.sam > ./data/9827_rand3.cram.fai: No such file or directory > ./compare_sam.pl ./data/9827_rand3.sam test.out/9827_rand3.scramble.sam > PASS: java.test > ==================== > 2 of 11 tests failed > ==================== > make[3]: *** [Makefile:529: check-TESTS] Error 1 > make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests' > make[2]: *** [Makefile:657: check-am] Error 2 > make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests' > make[1]: *** [Makefile:759: check-recursive] Error 1 > make[1]: Leaving directory '/<<PKGBUILDDIR>>' > dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 > returned exit code 2 The full build log is available from: http://qa-logs.debian.net/2022/10/23/staden-io-lib_1.14.14+dfsg-1_unstable.log All bugs filed during this archive rebuild are listed at: https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20221023;users=lu...@debian.org or: https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20221023&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! If you reassign this bug to another package, please marking it as 'affects'-ing this package. See https://www.debian.org/Bugs/server-control#affects If you fail to reproduce this, please provide a build log and diff it with mine so that we can identify if something relevant changed in the meantime.
