From 5cdd7a7ba4e34149fe966de06965ba1012fd74a1 Mon Sep 17 00:00:00 2001 From: kshakir Date: Wed, 27 Oct 2010 20:39:03 +0000 Subject: [PATCH] There's no such thing as a sam index, so the GATK extension generator doesn't need to add an @Input for them. Updated a call to swapExt to specify the directory. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4586 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/queue/extensions/gatk/ArgumentDefinitionField.java | 5 ++--- scala/qscript/fullCallingPipeline.q | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java index cc24af84a..4aaba7cc1 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java @@ -343,7 +343,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { private static class IndexFilesField extends ArgumentField { @Override protected Class getAnnotationIOClass() { return Input.class; } @Override public String getCommandLineAddition() { return ""; } - @Override protected String getDoc() { return "Dependencies on any index files for any bams or sams added to input_files"; } + @Override protected String getDoc() { return "Dependencies on any index files for any bams added to input_files"; } @Override protected String getFullName() { return "index_files"; } @Override protected boolean isRequired() { return false; } @Override protected String getFieldType() { return "List[File]"; } @@ -352,8 +352,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField { @Override protected String getRawFieldName() { return "index_files"; } @Override protected String getFreezeFields() { return String.format( - "index_files ++= input_file.filter(bam => bam != null && bam.getName.endsWith(\".bam\")).map(bam => new File(bam.getPath + \".bai\"))%n" + - "index_files ++= input_file.filter(sam => sam != null && sam.getName.endsWith(\".sam\")).map(sam => new File(sam.getPath + \".sai\"))%n"); + "index_files ++= input_file.filter(bam => bam != null && bam.getName.endsWith(\".bam\")).map(bam => new File(bam.getPath + \".bai\"))%n"); } } diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index d5b291808..5aa9b89e9 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -125,7 +125,7 @@ class fullCallingPipeline extends QScript { realigner.intervalsString = Nil realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size realigner.DBSNP = qscript.pipeline.getProject.getDbsnpFile - realigner.rodbind :+= RodBind("indels", "VCF", swapExt(qscript.pipeline.getProject.getReferenceFile, "fasta", "1kg_pilot_indels.vcf") + realigner.rodBind :+= RodBind("indels", "VCF", swapExt(realigner.reference_sequence.getParentFile, realigner.reference_sequence, "fasta", "1kg_pilot_indels.vcf")) // if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates if (realigner.scatterCount > 1) {