Java JNI bindings for BWA(mem-lite)

Motivation

BWA 7.4(http://bio-bwa.sourceforge.net/) contains a small C example(https://github.com/lh3/bwa/blob/master/example.c) for running bwa-mem as a library (bwamem-lite). I created some JNI bindings to see if I can bind the C bwa library to java and get the same output than bwamem-lite. I put the code on github at https://github.com/lindenb/jbwa.

Example

(compare to https://github.com/lh3/bwa/blob/master/example.c )

System.loadLibrary("bwajni");
BwaIndex index=new BwaIndex(new File("hg19.fa"));
BwaMem mem=new BwaMem(index);
KSeq kseq=new KSeq(new File("input.fastq.gz");
ShortRead read=null;
while((read=kseq.next())!=null)
        {
        for(AlnRgn a: mem.align(read))
                {
                if(a.getSecondary()>=0) continue;
                System.out.println(  read.getName()+"\t"+  a.getStrand()+"\t"+  a.getChrom()+"\t"+
                        a.getPos()+"\t"+ a.getMQual()+"\t"+ a.getCigar()+"\t"+  a.getNm() );
                }
        }
kseq.dispose();
index.close();
mem.dispose();

Testing

Here is the ouput of the JAVA version:

gunzip -c input.fastq.gz | head -n 4000 |\
java  -Djava.library.path=src/main/native -cp src/main/java \
   com.github.lindenb.jbwa.jni.Example human_g1k_v37.fasta -| tail 


HWI-1KL149:20:C1CU7ACXX:4:1101:3077:33410       +       3       38647538        60      89M11S  1
HWI-1KL149:20:C1CU7ACXX:4:1101:3396:33445       +       8       52567289        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:10013:33288      -       1       156104115       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:10390:33496      -       6       123824853       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:13537:33483      +       2       157367092       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:14139:33390      +       20      31413797        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:14514:33458      +       2       179401813       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:15292:33282      +       15      63335820        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:16960:33276      -       12      110782784       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:17355:33322      +       6       126077895       60      100M    1

And the ouput of the Native C version:

gunzip -c input.fastq.gz | head -n 4000 |\
bwa-0.7.4/bwamem-lite human_g1k_v37.fasta - | tail 

HWI-1KL149:20:C1CU7ACXX:4:1101:3077:33410       +       3       38647538        60      89M11S  1
HWI-1KL149:20:C1CU7ACXX:4:1101:3396:33445       +       8       52567289        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:10013:33288      -       1       156104115       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:10390:33496      -       6       123824853       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:13537:33483      +       2       157367092       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:14139:33390      +       20      31413797        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:14514:33458      +       2       179401813       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:15292:33282      +       15      63335820        60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:16960:33276      -       12      110782784       60      100M    1
HWI-1KL149:20:C1CU7ACXX:4:1101:17355:33322      +       6       126077895       60      100M    1

GUI

As a test I also created a swing-Based interface for BWA:

java  -Djava.library.path=src/main/native  -cp src/main/java \
    com.github.lindenb.jbwa.jni.BwaFrame human_g1k_v37.fasta

That's it,


Pierre