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now output in the exact format that works with sequenom software. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1798 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
jmaguire 2009-10-08 20:06:27 +00:00
parent 98e3a0bf1a
commit 8fdb8922b8
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java
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@ -80,9 +80,9 @@ public class PickSequenomProbes extends RefWalker<String, String>
if (snp != null) if (snp != null)
{ {
String snp_string = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases); String assay_sequence = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases);
String fasta_string = new String(">" + context.getLocation().toString() + "_" + ref.getWindow().toString()); String assay_id = new String(context.getLocation().toString() + "_" + ref.getWindow().toString()).replace(':', '_');
return fasta_string + "\n" + snp_string + "\n"; return assay_id + "\t" + assay_sequence + "\n";
} }
else else
{ {