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add _gI and _gD to the indel probe names according to the spec (in the hope that wiki is not obsolete); added optional cmd line param -project_id to prefix all probe names with. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2704 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-01-27 17:06:49 +00:00
parent ed9b7edee3
commit 3edcefb7fb
1 changed files with 14 additions and 3 deletions
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17
java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
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@ -22,7 +22,8 @@ import java.util.*;
public class PickSequenomProbes extends RefWalker<String, String> { public class PickSequenomProbes extends RefWalker<String, String> {
@Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's") @Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's")
protected String SNP_MASK = null; protected String SNP_MASK = null;
@Argument(required=false, shortName="project_id",doc="If specified, all probenames will be prepended with 'project_id|'")
String project_id = null;
private byte [] maskFlags = new byte[401]; private byte [] maskFlags = new byte[401];
private SeekableRODIterator<TabularROD> snpMaskIterator=null; private SeekableRODIterator<TabularROD> snpMaskIterator=null;
@ -103,8 +104,18 @@ public class PickSequenomProbes extends RefWalker<String, String> {
else else
return ""; return "";
String assay_id = new String(context.getLocation().toString() + "_" + ref.getWindow().toString()).replace(':', '_'); StringBuilder assay_id = new StringBuilder();
return assay_id + "\t" + assay_sequence + "\n"; if ( project_id != null ) {
assay_id.append(project_id);
assay_id.append('|');
}
assay_id.append(context.getLocation().toString().replace(':','_'));
assay_id.append('_');
if ( variant.isInsertion() ) assay_id.append("gI_");
else if ( variant.isDeletion()) assay_id.append("gD_");
assay_id.append(ref.getWindow().toString().replace(':', '_'));
return assay_id.toString() + "\t" + assay_sequence + "\n";
} }
public String reduceInit() { public String reduceInit() {