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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
This commit is contained in:
kshakir 2010-10-27 20:39:03 +00:00
parent 4c23b1fe9c
commit 5cdd7a7ba4
2 changed files with 3 additions and 4 deletions
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5
java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
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@ -343,7 +343,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
private static class IndexFilesField extends ArgumentField {
@Override protected Class<? extends Annotation> 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");
}
}

2
scala/qscript/fullCallingPipeline.q
View File

@ -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) {