From 380cd671468a01b0e431bf8d541051f00986260b Mon Sep 17 00:00:00 2001 From: Michael Linderman Date: Mon, 18 Aug 2014 18:54:26 -0400 Subject: [PATCH] Update extension generator to recognize RodBindingCollection as 'taggable' Signed-off-by: Khalid Shakir --- .../gatk/queue/extensions/gatk/ArgumentDefinitionField.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java index c9966c6d0..c410c9748 100644 --- a/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/public/gatk-queue-extensions-generator/src/main/java/org/broadinstitute/gatk/queue/extensions/gatk/ArgumentDefinitionField.java @@ -147,7 +147,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { } else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) { 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)); } else if (argumentDefinition.ioType == ArgumentIOType.INPUT) { @@ -416,7 +416,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { if (originalSuffix == null) { return String.format( ("%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"), indexFieldName, originalFieldName, indexSuffix); } else {