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

Compute and cache the length of the longest deletion observed at the site; ReadBackedExtendedEventPileup now has a getter to access that value. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2487 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-12-30 21:19:39 +00:00
parent 9c41ac252f
commit 89791d730e
2 changed files with 24 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
View File

@ -320,15 +320,21 @@ public class LocusIteratorByState extends LocusIterator {
if ( readInfo.generateExtendedEvents() && hasExtendedEvents ) {
ArrayList<ExtendedEventPileupElement> indelPile = new ArrayList<ExtendedEventPileupElement>(readStates.size());
int maxDeletionLength = 0;
for ( SAMRecordState state : readStates ) {
if ( state.hadIndel() ) {
size++;
if ( state.getEventBases() == null ) nDeletions++;
if ( state.getEventBases() == null ) {
nDeletions++;
maxDeletionLength = Math.max(maxDeletionLength,state.getEventLength());
}
else nInsertions++;
indelPile.add ( new ExtendedEventPileupElement(state.getRead(),
state.getReadEventStartOffset(),
state.getEventLength(),
state.getEventBases()) );
} else {
if ( state.getCurrentCigarOperator() != CigarOperator.N ) {
// this read has no indel associated with the previous position on the ref;
@ -358,7 +364,7 @@ public class LocusIteratorByState extends LocusIterator {
GenomeLoc loc = GenomeLocParser.incPos(our1stState.getLocation(),-1);
// System.out.println("Indel(s) at "+loc);
// for ( ExtendedEventPileupElement pe : indelPile ) { if ( pe.isIndel() ) System.out.println(" "+pe.toString()); }
return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, nInsertions, nDeletions, nMQ0Reads));
return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, indelPile, size, maxDeletionLength, nInsertions, nDeletions, nMQ0Reads));
} else {
ArrayList<PileupElement> pile = new ArrayList<PileupElement>(readStates.size());

17
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileup.java
View File

@ -20,6 +20,7 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
private ArrayList<ExtendedEventPileupElement> pileup = null;
private int size = 0; // cached value of the size of the pileup
private int maxDeletionLength = 0; // cached value of the length of the longest deletion observed at the site
private int nDeletions = 0; // cached value of the number of deletions
private int nInsertions = 0;
private int nMQ0Reads = 0; // cached value of the number of MQ0 reads
@ -53,13 +54,15 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
* @param loc
* @param pileup
*/
public ReadBackedExtendedEventPileup(GenomeLoc loc, ArrayList<ExtendedEventPileupElement> pileup, int size, int nInsertions, int nDeletions, int nMQ0Reads ) {
public ReadBackedExtendedEventPileup(GenomeLoc loc, ArrayList<ExtendedEventPileupElement> pileup, int size,
int maxDeletionLength, int nInsertions, int nDeletions, int nMQ0Reads ) {
if ( loc == null ) throw new StingException("Illegal null genomeloc in ReadBackedExtendedEventPileup");
if ( pileup == null ) throw new StingException("Illegal null pileup in ReadBackedExtendedEventPileup");
this.loc = loc;
this.pileup = pileup;
this.size = size;
this.maxDeletionLength = maxDeletionLength;
this.nDeletions = nDeletions;
this.nInsertions = nInsertions;
this.nMQ0Reads = nMQ0Reads;
@ -78,9 +81,11 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
nMQ0Reads = 0;
for ( ExtendedEventPileupElement p : this ) {
size++;
if ( p.isDeletion() ) {
nDeletions++;
maxDeletionLength = Math.max(maxDeletionLength, p.getEventLength());
} else {
if ( p.isInsertion() ) nInsertions++;
}
@ -200,6 +205,16 @@ public class ReadBackedExtendedEventPileup implements Iterable<ExtendedEventPile
return nInsertions;
}
/** Returns the length of the longest deletion observed at the site this
* pileup is associated with (NOTE: by convention, both insertions and deletions
* are associated with genomic location immediately before the actual event). If
* there are no deletions at the site, returns 0.
* @return
*/
public int getMaxDeletionLength() {
return maxDeletionLength;
}
/**
* Returns the number of mapping quality zero reads in this pileup.
* @return