debdiff staden-io-lib_1.13.5-1.dsc staden-io-lib_1.13.5-1.1.dsc diff -Nru staden-io-lib-1.13.5/debian/changelog staden-io-lib-1.13.5/debian/changelog --- staden-io-lib-1.13.5/debian/changelog 2014-03-15 03:07:55.000000000 +0000 +++ staden-io-lib-1.13.5/debian/changelog 2014-04-01 04:20:39.000000000 +0100 @@ -1,3 +1,13 @@ +staden-io-lib (1.13.5-1.1) unstable; urgency=medium + + * Non-maintainer upload. + * Fix io_lib/bam.c read + Patch by Aleksandar Zlicic + Add fix-bam-read.patch + Closes: #736565 + + -- Anibal Monsalve Salazar <ani...@debian.org> Tue, 01 Apr 2014 04:19:52 +0100 + staden-io-lib (1.13.5-1) unstable; urgency=medium * New upstream release. diff -Nru staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch --- staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch 1970-01-01 01:00:00.000000000 +0100 +++ staden-io-lib-1.13.5/debian/patches/fix-bam-read.patch 2014-04-01 04:19:23.000000000 +0100 @@ -0,0 +1,36 @@ +Date: Mon, 31 Mar 2014 19:22:13 +0200 +From: Aleksandar Zlicic <aleksandar.zli...@imgtec.com> +Subject: staden-io-lib: fix io_lib/bam.c read + +https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565 + +We have fixed a bug reported for the staden-io-lib package +(https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=736565). The cause +of this problem is an error in function bam_get_seq(), or to be more +precise, function's implementation for non-intel architectures. + +Function bam_get_seq is used for reading data from alignment blocks in +BAM files, block by block. + +In special cases, when the alignment block being read is the last +block in BAM file, and the block has no cigar operations and segment +sequence stored inside of it, function incorrectly detects +end-of-file. + +In that case, block has actually been successfully read, but because +of erroneous end-of-file detection, it isn't written to output file in +SAM format. + +Attached patch fixes this issue. + +--- a/io_lib/bam.c 2014-01-07 17:01:12.000000000 +0000 ++++ bio_lib//bam.c 2014-04-01 04:05:16.762660873 +0100 +@@ -1635,7 +1635,7 @@ int bam_get_seq(bam_file_t *b, bam_seq_t + + /* The remainder, word aligned */ + blk_size = blk_ret; +- if ((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0) ++ if (((blk_ret = bam_read(b, (char *)bam_cigar(bs), blk_size+4)) == 0) && blk_size != 0) + return 0; + if (blk_size+4 != blk_ret) { + if (blk_size != blk_ret) { diff -Nru staden-io-lib-1.13.5/debian/patches/series staden-io-lib-1.13.5/debian/patches/series --- staden-io-lib-1.13.5/debian/patches/series 2014-03-11 23:05:36.000000000 +0000 +++ staden-io-lib-1.13.5/debian/patches/series 2014-04-01 04:17:07.000000000 +0100 @@ -1 +1,2 @@ pathmax.patch +fix-bam-read.patch
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