Hi All,

I want to extract all reads containing a variant from a co-ordinate sorted bam file. The variant is an 11 bp long insertion starting at base position 39. I am running samjdk.jar script as per instructions in the post here: How to extract reads with a known variant form a bam file

I modified the input file Scripts.js like this:

final String contig= "ref";
final int mutpos = 39;
***final String mutbase="GCCCGGGCAAA";***
if(record.getReadUnmappedFlag()) return false;
if(!record.getContig().equals(contig)) return false;
if(record.getEnd() < mutpos) return false;
if(record.getStart() > mutpos) return false;
int readpos = record.getReadPositionAtReferencePosition(mutpos);
if(readpos<1) return false;
readpos--;
final byte[]    bases= record.getReadBases();
if(bases[readpos]==mutbase) return true;
return false;

I am getting the following error.

/

tmp/jvarkit4226389813265542455.tmp/SamJdkCustom61691149.java:25: error: bad operand types for binary operator '=='
if(bases[readpos]==mutbase) return true;
                 ^
  first type:  byte
  second type: String
1 error
[SEVERE][SamJdk]java.lang.RuntimeException: Cannot compile
java.lang.RuntimeException: java.lang.RuntimeException: Cannot compile
    at com.github.lindenb.jvarkit.lang.OpenJdkCompiler$DefaultOpenJdkCompiler.compileClass(OpenJdkCompiler.java:255)
    at com.github.lindenb.jvarkit.tools.samjs.SamJdk.doWork(SamJdk.java:568)
    at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:736)
    at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:894)
    at com.github.lindenb.jvarkit.tools.samjs.SamJdk.main(SamJdk.java:785)
Caused by: java.lang.RuntimeException: Cannot compile
    at com.github.lindenb.jvarkit.lang.OpenJdkCompiler$DefaultOpenJdkCompiler.exec(OpenJdkCompiler.java:180)
    at com.github.lindenb.jvarkit.lang.OpenJdkCompiler$DefaultOpenJdkCompiler.compileClass(OpenJdkCompiler.java:232)
    ... 4 more
[INFO][Launcher]samjdk Exited with failure (-1)

How can I resolve this error? This is occurring due to difference in character and string operators in java. Can Samjdk be used for indels?

Thanks in advance !!