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added capability for filtering by platform 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1011 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-15 19:19:50 +00:00
parent 8f4bc8cb6e
commit 11aa715630
1 changed files with 26 additions and 1 deletions
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27
java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers; package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMFileWriter; import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.cmdLine.Argument;
@ -49,6 +50,17 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
String outputBamFile = null; String outputBamFile = null;
@Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false) @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false)
Integer maxLength = null; Integer maxLength = null;
@Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
String platform = null;
// E.g. ILLUMINA, 454
/**
* The initialize function.
*/
public void initialize() {
if ( platform != null )
platform = platform.toUpperCase();
}
/** /**
* The reads filter function. * The reads filter function.
@ -57,7 +69,20 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* @return true if the read passes the filter, false if it doesn't * @return true if the read passes the filter, false if it doesn't
*/ */
public boolean filter(char[] ref, SAMRecord read) { public boolean filter(char[] ref, SAMRecord read) {
return (maxLength == null || read.getReadLength() <= maxLength); if ( maxLength != null && read.getReadLength() > maxLength )
return false;
if ( platform != null ) {
Object readGroupAttr = read.getAttribute("RG");
if ( readGroupAttr != null ) {
SAMReadGroupRecord readGroup = getToolkit().getEngine().getSAMHeader().getReadGroup(readGroupAttr.toString());
if ( readGroup != null ) {
Object readPlatformAttr = readGroup.getAttribute("PL");
if ( readPlatformAttr != null )
return readPlatformAttr.toString().toUpperCase().contains(platform);
}
}
}
return true;
} }
/** /**