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Optimization: LocusReferenceView now passes along the contig index to createGenomeLoc, speeding up their creation 

-- Also cleaned up some unused methods
This commit is contained in:
Mark DePristo 2013-01-25 17:21:05 -05:00
parent 52a28968a9
commit 93d88cdc68
1 changed files with 3 additions and 40 deletions
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43
public/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
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@ -123,38 +123,10 @@ public class LocusReferenceView extends ReferenceView {
if(bounds != null) {
int expandedStart = getWindowStart( bounds );
int expandedStop = getWindowStop( bounds );
initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), expandedStart, expandedStop));
initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), bounds.getContigIndex(), expandedStart, expandedStop));
}
}
/** Returns true if the specified location is fully within the bounds of the reference window loaded into
* this LocusReferenceView object.
*/
public boolean isLocationWithinBounds(GenomeLoc loc) {
return bounds.containsP(loc);
}
/** Ensures that specified location is within the bounds of the reference window loaded into this
* LocusReferenceView object. If the location loc is within the current bounds (or if it is null), then nothing is done.
* Otherwise, the bounds are expanded on either side, as needed, to accomodate the location, and the reference seuqence for the
* new bounds is reloaded (can be costly!). If loc spans beyond the current contig, the expansion is performed
* to the start/stop of that contig only.
* @param loc
*/
public void expandBoundsToAccomodateLoc(GenomeLoc loc) {
if ( bounds==null || loc==null) return; // can bounds be null actually???
if ( isLocationWithinBounds(loc) ) return;
if ( loc.getContigIndex() != bounds.getContigIndex() )
throw new ReviewedStingException("Illegal attempt to expand reference view bounds to accommodate location on a different contig.");
bounds = genomeLocParser.createGenomeLoc(bounds.getContig(),
Math.min(bounds.getStart(),loc.getStart()),
Math.max(bounds.getStop(),loc.getStop()));
int expandedStart = getWindowStart( bounds );
int expandedStop = getWindowStop( bounds );
initializeReferenceSequence(genomeLocParser.createGenomeLoc(bounds.getContig(), expandedStart, expandedStop));
}
/**
* Initialize the bounds of this shard, trimming the bounds so that they match the reference.
* @param provider Provider covering the appropriate locus.
@ -210,7 +182,8 @@ public class LocusReferenceView extends ReferenceView {
public ReferenceContext getReferenceContext( GenomeLoc genomeLoc ) {
//validateLocation( genomeLoc );
GenomeLoc window = genomeLocParser.createGenomeLoc( genomeLoc.getContig(), getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
GenomeLoc window = genomeLocParser.createGenomeLoc( genomeLoc.getContig(), bounds.getContigIndex(),
getWindowStart(genomeLoc), getWindowStop(genomeLoc) );
int refStart = -1;
if (bounds != null) {
@ -237,16 +210,6 @@ public class LocusReferenceView extends ReferenceView {
return super.getReferenceBases(genomeLoc);
}
/**
* Validates that the genomeLoc is one base wide and is in the reference sequence.
* @param genomeLoc location to verify.
*/
private void validateLocation( GenomeLoc genomeLoc ) throws InvalidPositionException {
if( bounds != null && !bounds.containsP(genomeLoc) )
throw new InvalidPositionException(
String.format("Requested position %s not within interval %s", genomeLoc, bounds));
}
/**
* Gets the start of the expanded window, bounded if necessary by the contig.
* @param locus The locus to expand.