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Only prints about first contig info setting 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@574 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-04-30 22:14:26 +00:00
parent 1cc5e74435
commit 12d6edfe7c
1 changed files with 13 additions and 1 deletions
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14
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -74,7 +74,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs"); logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
Utils.scareUser("Failed to load reference dictionary"); Utils.scareUser("Failed to load reference dictionary");
return false; return false;
} else { } else if ( contigInfo == null ){
contigInfo = seqDict; contigInfo = seqDict;
logger.debug(String.format("Prepared reference sequence contig dictionary")); logger.debug(String.format("Prepared reference sequence contig dictionary"));
for (SAMSequenceRecord contig : seqDict.getSequences() ) { for (SAMSequenceRecord contig : seqDict.getSequences() ) {
@ -450,6 +450,18 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
n.incPos(); n.incPos();
return n; return n;
} }
// Dangerous
// public boolean equals(Object o) {
// // Not strictly necessary, but often a good optimization
// if (this == o)
// return true;
// if (!(o instanceof GenomeLoc))
// return false;
// else
// return compareContigs((GenomeLoc)o) == 0;
// }
// //
// Comparison operations // Comparison operations
// //