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add a little bit of documentation to the RMD track builder and wrap any exceptions thrown in tribble with the file source and line that caused the error. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4243 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-09-09 17:56:36 +00:00
parent aeb897db7f
commit f5c295b6b2
1 changed files with 12 additions and 0 deletions
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12
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
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@ -107,6 +107,12 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
return new TribbleTrack(targetClass, name, inputFile, pair.first, pair.second, createCodec(targetClass, name)); return new TribbleTrack(targetClass, name, inputFile, pair.first, pair.second, createCodec(targetClass, name));
} }
/**
* create a tribble feature reader class, given the target class and the input file
* @param targetClass the target class, of a Tribble Codec type
* @param inputFile the input file, that corresponds to the feature type
* @return a pair of <BasicFeatureSource, SAMSequenceDictionary>
*/
public Pair<BasicFeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, File inputFile) { public Pair<BasicFeatureSource, SAMSequenceDictionary> createFeatureReader(Class targetClass, File inputFile) {
return createFeatureReader(targetClass, "anonymous", inputFile); return createFeatureReader(targetClass, "anonymous", inputFile);
} }
@ -147,6 +153,12 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
} }
} }
/**
* add a name to the codec, if it takes one
* @param targetClass the class to create a codec for
* @param name the name to assign this codec
* @return the feature codec itself
*/
private FeatureCodec createCodec(Class targetClass, String name) { private FeatureCodec createCodec(Class targetClass, String name) {
FeatureCodec codex = this.createByType(targetClass); FeatureCodec codex = this.createByType(targetClass);
if ( codex instanceof NameAwareCodec ) if ( codex instanceof NameAwareCodec )