From b446b3f1b6b6022ef20452bf6d5540c364fcbd4f Mon Sep 17 00:00:00 2001 From: sjia Date: Wed, 23 Sep 2009 21:13:52 +0000 Subject: [PATCH] CreateHaplotypeWalker now gives correct output git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1709 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/HLAcaller/CreateHaplotypesWalker.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java index 27652aa47..61706c686 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java @@ -58,17 +58,18 @@ public class CreateHaplotypesWalker extends ReadWalker { String s = formatter.FormatRead(read.getCigarString(),read.getReadString()); String name = read.getReadName(); - out.printf("%s->%s HAPLO01",name,name); + out.printf("%s->%s HAPLO01 ",name,name); + for (int i = start; i <= end; i++){ - if (i - readstart < s.length() && i - readstart >= 0){ + if (i - readstart < s.length()){ c = s.charAt(i-readstart); out.printf("%s",indexer.get(c)); }else{ out.print("0"); } } - out.print("\n"); + out.printf("\n"); } return 1; } @@ -83,7 +84,7 @@ public class CreateHaplotypesWalker extends ReadWalker { public void onTraversalDone(Integer value) { out.print("\nSNP names:\n"); for (int pos = start; pos <= end; pos++){ - SNPname = "CHR6POS" + String.valueOf(pos); + SNPname = "CHR6_POS" + String.valueOf(pos); SNPnames[pos-start]=SNPname; out.printf("%s\n",SNPname); }