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Update extension generator to recognize RodBindingCollection as 'taggable' 

Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
This commit is contained in:
Michael Linderman 2014-08-18 18:54:26 -04:00 committed by Khalid Shakir
parent 46b0c18603
commit 380cd67146
1 changed files with 2 additions and 2 deletions
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4
public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -147,7 +147,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
} else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) { } else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, BAMIndex.BAMIndexSuffix, ".bam")); return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, BAMIndex.BAMIndexSuffix, ".bam"));
} else if ((RodBinding.class.equals(argumentDefinition.argumentType) || RodBinding.class.equals(argumentDefinition.componentType)) && argumentDefinition.ioType == ArgumentIOType.INPUT) { } else if ((RodBinding.class.equals(argumentDefinition.argumentType) || RodBinding.class.equals(argumentDefinition.componentType) || RodBindingCollection.class.equals(argumentDefinition.componentType)) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION)); return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new InputIndexesArgumentField(argumentDefinition, Tribble.STANDARD_INDEX_EXTENSION));
} else if (argumentDefinition.ioType == ArgumentIOType.INPUT) { } else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
@ -416,7 +416,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
if (originalSuffix == null) { if (originalSuffix == null) {
return String.format( return String.format(
("%1$s ++= %2$s" + ("%1$s ++= %2$s" +
".filter(orig => orig != null)" + ".filter(orig => orig != null && (!orig.getName.endsWith(\".list\")))" +
".map(orig => new File(orig.getPath + \"%3$s\"))%n"), ".map(orig => new File(orig.getPath + \"%3$s\"))%n"),
indexFieldName, originalFieldName, indexSuffix); indexFieldName, originalFieldName, indexSuffix);
} else { } else {