From 9c4fc633aa4b9a21c9f7561f0f958acd27e57761 Mon Sep 17 00:00:00 2001 From: asivache Date: Tue, 7 Apr 2009 21:44:39 +0000 Subject: [PATCH] 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 --- java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 7cb725508..fc47c01a3 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -94,9 +94,10 @@ public class GenomeLoc implements Comparable { } 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; - else { + } else { contigInfo = seqDict; logger.info(String.format("Prepared reference sequence contig dictionary%n order ->")); for (SAMSequenceRecord contig : seqDict.getSequences() ) { @@ -196,7 +197,7 @@ public class GenomeLoc implements Comparable { } 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; }