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Refactored to clean it up a bit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@495 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-04-22 19:18:46 +00:00
parent 1bf4d040d8
commit d99d67d51c
1 changed files with 8 additions and 6 deletions
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14
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java
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@ -15,18 +15,20 @@ public class ReadFilterWalker extends ReadWalker<Integer,Integer> {
@Argument(fullName="output_file", shortName="O",doc="SAM or BAM file to write filtered reads into (will be overwritten if exists)",required=true ) public String output; @Argument(fullName="output_file", shortName="O",doc="SAM or BAM file to write filtered reads into (will be overwritten if exists)",required=true ) public String output;
@Argument(fullName="max_read_length",doc="Discard reads with length greater than the specified value",required=false) public Integer max_len; @Argument(fullName="max_read_length",doc="Discard reads with length greater than the specified value",required=false) public Integer max_len;
private SAMFileWriter writer = null; private SAMFileWriter writer = null;
public void initialize() {
SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, header.getSortOrder() != SAMFileHeader.SortOrder.unsorted, new File(output));
}
@Override @Override
public boolean filter(LocusContext context, SAMRecord read) { public boolean filter(LocusContext context, SAMRecord read) {
if ( read.getReadLength() > max_len ) return false; return read.getReadLength() <= max_len;
return true;
} }
@Override @Override
public Integer map(LocusContext context, SAMRecord read) { public Integer map(LocusContext context, SAMRecord read) {
if ( writer == null ) writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(read.getHeader(), read.getHeader().getSortOrder() != SAMFileHeader.SortOrder.unsorted, new File(output));
writer.addAlignment(read); writer.addAlignment(read);
return 1; return 1;
} }
@ -42,8 +44,8 @@ public class ReadFilterWalker extends ReadWalker<Integer,Integer> {
} }
public void onTraversalDone(Integer nReads) { public void onTraversalDone(Integer nReads) {
super.onTraversalDone(nReads); writer.close();
out.println(nReads +" reads passed the filter and were written into output file "+output); out.println(nReads +" reads passed the filter and were written into output file "+output);
} }
} }