Hi,
I tried to follow the procedure Olivier has described for IGV and pushed
this to Git - but I was not that lucky. Besides I needed to do one patch
there is one remaining problem my poor skills are not sufficient for:
build-project:
[echo] FastQC: /build/fastqc-0.11.4+dfsg/build.xml
[javac] Compiling 68 source files to /build/fastqc-0.11.4+dfsg/bin
[javac] warning: [options] bootstrap class path not set in conjunction with
-source 1.5
[javac]
/build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java:58:
error: cannot find symbol
[javac]
SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
[javac]
^
[javac] symbol: variable ValidationStringency
[javac] location: class SAMFileReader
[javac] Note:
/build/fastqc-0.11.4+dfsg/uk/ac/babraham/FastQC/Sequence/BAMFile.java uses or
overrides a deprecated API.
[javac] Note: Recompile with -Xlint:deprecation for details.
[javac] Note: Some input files use unchecked or unsafe operations.
[javac] Note: Recompile with -Xlint:unchecked for details.
[javac] 1 error
[javac] 1 warning
My obviously poor try
--- a/debian/patches/adapt_to_htslib.patch
+++ b/debian/patches/adapt_to_htslib.patch
@@ -23,3 +23,12 @@ Description: Path to samtools changed when switching from
libsam-java
public class BAMFile implements SequenceFile {
+@@ -55,7 +55,7 @@ public class BAMFile implements Sequence
+ name = file.getName();
+ this.onlyMapped = onlyMapped;
+
+-
SAMFileReader.setDefaultValidationStringency(SAMFileReader.ValidationStringency.SILENT);
++
SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
+
+ fis = new FileInputStream(file);
+
did not changed anything.
Any hint?
Kind regards
Andreas.
--
http://fam-tille.de
