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Make it symmetric: if there is no sequence dictionary, also send a message to the logger, just like we do when we find the dict 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@318 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-07 21:44:39 +00:00
parent b64e4d1a04
commit 9c4fc633aa
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
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@ -94,9 +94,10 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
} }
public static boolean setupRefContigOrdering(final SAMSequenceDictionary seqDict) { public static boolean setupRefContigOrdering(final SAMSequenceDictionary seqDict) {
if (seqDict == null) // we couldn't load the reference dictionary if (seqDict == null) { // we couldn't load the reference dictionary
logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
return false; return false;
else { } else {
contigInfo = seqDict; contigInfo = seqDict;
logger.info(String.format("Prepared reference sequence contig dictionary%n order ->")); logger.info(String.format("Prepared reference sequence contig dictionary%n order ->"));
for (SAMSequenceRecord contig : seqDict.getSequences() ) { for (SAMSequenceRecord contig : seqDict.getSequences() ) {
@ -196,7 +197,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
} }
GenomeLoc loc = new GenomeLoc(contig, start, stop); GenomeLoc loc = new GenomeLoc(contig, start, stop);
//System.out.printf(" => Parsed location '%s' into %s%n", str, loc); // System.out.printf(" => Parsed location '%s' into %s%n", str, loc);
return loc; return loc;
} }