[Debian-med-packaging] Bug#810843: fastqc: libsam-java is gone

[Andreas Tille]

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