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Add option to adhere to the PlinkRod naming convention [ProjectName]|c[Chrom]_p[Pos] 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2927 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-03-04 18:31:27 +00:00
parent 0dd65461a1
commit a4d494c38b
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
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@ -28,6 +28,8 @@ public class PickSequenomProbes extends RefWalker<String, String> {
String project_id = null;
@Argument(required = false, shortName="omitWindow", doc = "If specified, the window appender will be omitted from the design files (e.g. \"_chr:start-stop\")")
boolean omitWindow = false;
@Argument(required = false, fullName="usePlinkRODNamingConvention", shortName="nameConvention",doc="Use the naming convention defined in PLINKROD")
boolean useNamingConvention = false;
private byte [] maskFlags = new byte[401];
@ -118,7 +120,12 @@ public class PickSequenomProbes extends RefWalker<String, String> {
assay_id.append(project_id);
assay_id.append('|');
}
assay_id.append(context.getLocation().toString().replace(':','_'));
if ( useNamingConvention ) {
assay_id.append('c');
assay_id.append(context.getLocation().toString().replace(":","_p"));
} else {
assay_id.append(context.getLocation().toString().replace(':','_'));
}
if ( variant.isInsertion() ) assay_id.append("_gI");
else if ( variant.isDeletion()) assay_id.append("_gD");