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Very bad use of the == operator with Strings was ensuring that validating GenomeLocs was very inefficient. This fix resulted in a significant speedup for a simple RodWalker.

This commit is contained in:
Eric Banks 2011-11-21 14:49:47 -05:00
parent b5de182014
commit 022832bd74
1 changed files with 2 additions and 2 deletions
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4
public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -87,12 +87,12 @@ public class GenomeLocParser {
@Requires("contig != null") @Requires("contig != null")
public synchronized boolean hasContig(final String contig) { public synchronized boolean hasContig(final String contig) {
return lastContig == contig || dict.getSequence(contig) != null; return contig.equals(lastContig) || dict.getSequence(contig) != null;
} }
@Requires("index >= 0") @Requires("index >= 0")
public synchronized boolean hasContig(final int index) { public synchronized boolean hasContig(final int index) {
return lastIndex == index|| dict.getSequence(index) != null; return lastIndex == index || dict.getSequence(index) != null;
} }
@Requires("contig != null") @Requires("contig != null")