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FIxed a nasty bug in GenomeLoc compareContigs; we were using '==' to compare Integer contig ID's. The surprising thing is that it actually works for Integers > -127 and < 128 (they're cached by the JVM, so it's actually comparing the underlying ints). Switched over GenomeLoc contigs to int based. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1033 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-17 20:19:47 +00:00
parent ed7fac1c90
commit b947fd586f
1 changed files with 7 additions and 3 deletions
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10
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -26,7 +26,7 @@ import java.util.regex.Pattern;
public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable { public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
private static Logger logger = Logger.getLogger(GenomeLoc.class); private static Logger logger = Logger.getLogger(GenomeLoc.class);
private Integer contigIndex; private int contigIndex;
private long start; private long start;
private long stop; private long stop;
@ -475,7 +475,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
return false; return false;
if(other instanceof GenomeLoc) { if(other instanceof GenomeLoc) {
GenomeLoc otherGenomeLoc = (GenomeLoc)other; GenomeLoc otherGenomeLoc = (GenomeLoc)other;
return this.contigIndex.equals(otherGenomeLoc.contigIndex) && return this.contigIndex == otherGenomeLoc.contigIndex &&
this.start == otherGenomeLoc.start && this.start == otherGenomeLoc.start &&
this.stop == otherGenomeLoc.stop; this.stop == otherGenomeLoc.stop;
} }
@ -546,7 +546,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
} }
public final int compareContigs( GenomeLoc that ) { public final int compareContigs( GenomeLoc that ) {
return (this.contigIndex == that.contigIndex)?0:((this.contigIndex < that.contigIndex)?-1:1); if (this.contigIndex == that.contigIndex)
return 0;
else if (this.contigIndex > that.contigIndex)
return 1;
return -1;
} }
public int compareTo( GenomeLoc that ) { public int compareTo( GenomeLoc that ) {