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fix for SSG with pl name 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1591 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-09-11 20:39:34 +00:00
parent 5354c1876c
commit 7c8b17b456
1 changed files with 2 additions and 1 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/EmpiricalSubstitutionGenotypeLikelihoods.java
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@ -43,7 +43,7 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
} }
public static SequencerPlatform standardizeSequencerPlatform( final String sequencerString ) { public static SequencerPlatform standardizeSequencerPlatform( final String sequencerString ) {
String lcSequencerString = sequencerString.toLowerCase(); String lcSequencerString = sequencerString == null ? null : sequencerString.toLowerCase();
if ( sequencerString != null && PLFieldToSequencerPlatform.containsKey(lcSequencerString) ) { if ( sequencerString != null && PLFieldToSequencerPlatform.containsKey(lcSequencerString) ) {
return PLFieldToSequencerPlatform.get(lcSequencerString); return PLFieldToSequencerPlatform.get(lcSequencerString);
} else { } else {
@ -259,6 +259,7 @@ public class EmpiricalSubstitutionGenotypeLikelihoods extends GenotypeLikelihood
throw new RuntimeException("Unknown Sequencer platform for read " + read.format()); throw new RuntimeException("Unknown Sequencer platform for read " + read.format());
else { else {
pl = defaultPlatform; pl = defaultPlatform;
//System.out.printf("Using default platform %s", pl);
} }
} }