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Cache result of getLocation() in Shard so we don't performance expensive calculation over and over

This commit is contained in:
Mark DePristo 2013-01-16 12:09:36 -05:00
parent 4d0e7b50ec
commit ddcb33fcf8
1 changed files with 26 additions and 16 deletions
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42
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/Shard.java
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@ -95,7 +95,10 @@ public abstract class Shard implements HasGenomeLocation {
*/ */
private final Map<SAMReaderID,SAMFileSpan> fileSpans; private final Map<SAMReaderID,SAMFileSpan> fileSpans;
/**
* Lazy-calculated span of all of the genome locs in this shard
*/
private GenomeLoc spanningLocation = null;
/** /**
* Statistics about which reads in this shards were used and which were filtered away. * Statistics about which reads in this shards were used and which were filtered away.
@ -148,27 +151,34 @@ public abstract class Shard implements HasGenomeLocation {
/** /**
* Returns the span of the genomeLocs comprising this shard * Returns the span of the genomeLocs comprising this shard
* @param * @return a GenomeLoc that starts as the first position in getGenomeLocs() and stops at the stop of the last
* @return * position in getGenomeLocs()
*/ */
public GenomeLoc getLocation() { public GenomeLoc getLocation() {
if ( getGenomeLocs() == null ) if ( spanningLocation == null ) {
return GenomeLoc.WHOLE_GENOME; if ( getGenomeLocs() == null )
spanningLocation = GenomeLoc.WHOLE_GENOME;
else if ( getGenomeLocs().size() == 0 ) {
spanningLocation = getGenomeLocs().get(0);
} else {
int start = Integer.MAX_VALUE;
int stop = Integer.MIN_VALUE;
String contig = null;
int start = Integer.MAX_VALUE; for ( GenomeLoc loc : getGenomeLocs() ) {
int stop = Integer.MIN_VALUE; if ( GenomeLoc.isUnmapped(loc) )
String contig = null; // special case the unmapped region marker, just abort out
return loc;
contig = loc.getContig();
if ( loc.getStart() < start ) start = loc.getStart();
if ( loc.getStop() > stop ) stop = loc.getStop();
}
for ( GenomeLoc loc : getGenomeLocs() ) { spanningLocation = parser.createGenomeLoc(contig, start, stop);
if ( GenomeLoc.isUnmapped(loc) ) }
// special case the unmapped region marker, just abort out
return loc;
contig = loc.getContig();
if ( loc.getStart() < start ) start = loc.getStart();
if ( loc.getStop() > stop ) stop = loc.getStop();
} }
return parser.createGenomeLoc(contig, start, stop); return spanningLocation;
} }