From 8fdb8922b86c040ae55ebc58edd7210244b970e4 Mon Sep 17 00:00:00 2001 From: jmaguire Date: Thu, 8 Oct 2009 20:06:27 +0000 Subject: [PATCH] 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 --- .../sting/playground/gatk/walkers/PickSequenomProbes.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java index 7e651c7d0..c2e95a9b6 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java @@ -80,9 +80,9 @@ public class PickSequenomProbes extends RefWalker if (snp != null) { - String snp_string = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases); - String fasta_string = new String(">" + context.getLocation().toString() + "_" + ref.getWindow().toString()); - return fasta_string + "\n" + snp_string + "\n"; + String assay_sequence = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases); + String assay_id = new String(context.getLocation().toString() + "_" + ref.getWindow().toString()).replace(':', '_'); + return assay_id + "\t" + assay_sequence + "\n"; } else {