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Cache pileup bases and mapping quals after first call to getBases() and getMappingQuals(), respectively. Subsequent calls to these method will return cached arrays. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2525 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-06 18:05:00 +00:00
parent d6fb19bb67
commit a17d725c35
1 changed files with 13 additions and 7 deletions
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18
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
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@ -20,6 +20,8 @@ import net.sf.samtools.SAMRecord;
public class ReadBackedPileup implements Iterable<PileupElement> { public class ReadBackedPileup implements Iterable<PileupElement> {
private GenomeLoc loc = null; private GenomeLoc loc = null;
private ArrayList<PileupElement> pileup = null; private ArrayList<PileupElement> pileup = null;
byte [] bases = null; // will be used to cache pileup bases after first call to getBases
byte [] mapquals = null; // will be used to cache pileup mapping quals after first call to getMappingQuals
private int size = 0; // cached value of the size of the pileup private int size = 0; // cached value of the size of the pileup
private int nDeletions = 0; // cached value of the number of deletions private int nDeletions = 0; // cached value of the number of deletions
@ -395,9 +397,11 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
* @return * @return
*/ */
public byte[] getBases() { public byte[] getBases() {
byte[] v = new byte[size()]; if ( bases == null ) {
for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { v[pile.getPileupOffset()] = pile.getBase(); } bases = new byte[size()];
return v; for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { bases[pile.getPileupOffset()] = pile.getBase(); }
}
return bases;
} }
/** /**
@ -425,9 +429,11 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
* @return * @return
*/ */
public byte[] getMappingQuals() { public byte[] getMappingQuals() {
byte[] v = new byte[size()]; if ( mapquals == null ) {
for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { v[pile.getPileupOffset()] = (byte)pile.getRead().getMappingQuality(); } mapquals = new byte[size()];
return v; for ( ExtendedPileupElement pile : this.extendedForeachIterator() ) { mapquals[pile.getPileupOffset()] = (byte)pile.getRead().getMappingQuality(); }
}
return mapquals;
} }