zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed deletion depth calculation plus mis-spelling in ReadBackedPileup method. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2315 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-10 21:11:42 +00:00
parent 31b1d60d28
commit 2869270c11
2 changed files with 3 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -205,7 +205,7 @@ public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genot
// are there too many deletions in the pileup? // are there too many deletions in the pileup?
ReadBackedPileup pileup = context.getPileup(); ReadBackedPileup pileup = context.getPileup();
if ( isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) && if ( isValidDeletionFraction(UAC.MAX_DELETION_FRACTION) &&
(double)pileup.getNumberOfDeletions() / (double)pileup.size() > UAC.MAX_DELETION_FRACTION ) (double)pileup.getPileupWithoutMappingQualityZeroReads().getNumberOfDeletions() / (double)(pileup.size() - pileup.getNumberOfMappingQualityZeroReads()) > UAC.MAX_DELETION_FRACTION )
return null; return null;
// stratify the AlignmentContext and cut by sample // stratify the AlignmentContext and cut by sample

4
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
View File

@ -382,7 +382,7 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
* Get an array of the mapping qualities * Get an array of the mapping qualities
* @return * @return
*/ */
public byte[] getMapppingQuals() { public byte[] getMappingQuals() {
byte[] v = new byte[size()]; byte[] v = new byte[size()];
for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { v[pile.getPileupOffset()] = (byte)pile.getRead().getMappingQuality(); } for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { v[pile.getPileupOffset()] = (byte)pile.getRead().getMappingQuality(); }
return v; return v;
@ -393,7 +393,7 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
// Private functions for printing pileups // Private functions for printing pileups
// //
private String getMappingQualsString() { private String getMappingQualsString() {
return quals2String(getMapppingQuals()); return quals2String(getMappingQuals());
} }
private static String quals2String( byte[] quals ) { private static String quals2String( byte[] quals ) {