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added a quick option to print the first n reads. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5912 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-06-01 16:16:50 +00:00
parent a79967d9af
commit 8f3e8f934d
1 changed files with 11 additions and 2 deletions
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13
java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
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@ -51,8 +51,9 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName = "readGroup", shortName = "readGroup", doc="Discard reads not belonging to the specified read group", required = false) @Argument(fullName = "readGroup", shortName = "readGroup", doc="Discard reads not belonging to the specified read group", required = false)
String readGroup = null; String readGroup = null;
@Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false) @Argument(fullName = "platform", shortName = "platform", doc="Discard reads not generated by the specified platform", required = false)
String platform = null; String platform = null; // E.g. ILLUMINA, 454
// E.g. ILLUMINA, 454 @Argument(fullName = "number", shortName = "n", doc="Outputs only the first n reads, discarding the rest", required = false)
int nReadsToPrint = -1;
/** /**
* The initialize function. * The initialize function.
@ -87,6 +88,14 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
return false; return false;
} }
// check if we've reached the output limit
if ( nReadsToPrint == 0 ) {
return false; // n == 0 means we've printed all we needed.
}
else if (nReadsToPrint > 0) {
nReadsToPrint--; // n > 0 means there are still reads to be printed.
}
return true; return true;
} }