zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

CreateHaplotypeWalker now gives correct output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1709 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
sjia 2009-09-23 21:13:52 +00:00
parent eeb14ec717
commit b446b3f1b6
1 changed files with 5 additions and 4 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

9
java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/CreateHaplotypesWalker.java
View File

@ -58,17 +58,18 @@ public class CreateHaplotypesWalker extends ReadWalker<Integer, Integer> {
String s = formatter.FormatRead(read.getCigarString(),read.getReadString()); String s = formatter.FormatRead(read.getCigarString(),read.getReadString());
String name = read.getReadName(); 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++){ 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); c = s.charAt(i-readstart);
out.printf("%s",indexer.get(c)); out.printf("%s",indexer.get(c));
}else{ }else{
out.print("0"); out.print("0");
} }
} }
out.print("\n"); out.printf("\n");
} }
return 1; return 1;
} }
@ -83,7 +84,7 @@ public class CreateHaplotypesWalker extends ReadWalker<Integer, Integer> {
public void onTraversalDone(Integer value) { public void onTraversalDone(Integer value) {
out.print("\nSNP names:\n"); out.print("\nSNP names:\n");
for (int pos = start; pos <= end; pos++){ for (int pos = start; pos <= end; pos++){
SNPname = "CHR6POS" + String.valueOf(pos); SNPname = "CHR6_POS" + String.valueOf(pos);
SNPnames[pos-start]=SNPname; SNPnames[pos-start]=SNPname;
out.printf("%s\n",SNPname); out.printf("%s\n",SNPname);
} }