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Deal with bad input; also N-way out isn't default. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2823 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-02-11 03:44:56 +00:00
parent dc885ba386
commit a4a2c9b172
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -32,8 +32,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Argument(fullName="output", shortName="O", required=false, doc="Output bam (or directory if using --NwayOutput)")
protected String baseWriterFilename = null;
@Argument(fullName="NWayOutput", shortName="nway", required=false, doc="Should the reads be emitted in a separate bam file for each one of the input bams? [default:yes]")
protected boolean NWAY_OUTPUT = true;
@Argument(fullName="NWayOutput", shortName="nway", required=false, doc="Should the reads be emitted in a separate bam file for each one of the input bams? [default:no]")
protected boolean NWAY_OUTPUT = false;
@Argument(fullName="outputSuffix", shortName="suffix", required=false, doc="Suffix to append to output bams (when using --NwayOutput) [default:'.cleaned']")
protected String outputSuffix = "cleaned";
@ -279,8 +279,6 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
else { // the read is past the current interval
// TODO - NOW WE NEED TO GET THE APPROPRIATE KNOWN INDELS FOR THIS REGION
clean(readsToClean);
// merge the two sets for emission
@ -1205,6 +1203,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} else {
long lastPosWithRefBase = loc.getStart() + reference.length -1;
int neededBases = (int)(read.getAlignmentEnd() - lastPosWithRefBase);
if ( neededBases > ref.length )
throw new StingException("Read " + read.getReadName() + " does not overlap the previous read in this interval; please ensure that you are using the same input bam that was used in the RealignerTargetCreator step");
if ( neededBases > 0 ) {
char[] newReference = new char[reference.length + neededBases];
System.arraycopy(reference, 0, newReference, 0, reference.length);