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

* added a bit more debugging output 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@446 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-16 15:20:26 +00:00
parent d35a542bb9
commit 6f56938d42
1 changed files with 6 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
View File

@ -62,6 +62,7 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
List<SAMRecord> reads = context.getReads(); List<SAMRecord> reads = context.getReads();
int tumorDepth = 0; int tumorDepth = 0;
int normalDepth = 0; int normalDepth = 0;
StringBuilder readNames = new StringBuilder();
for ( int i = 0; i < reads.size(); i++ ) for ( int i = 0; i < reads.size(); i++ )
{ {
SAMRecord read = reads.get(i); SAMRecord read = reads.get(i);
@ -98,6 +99,7 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
} else { } else {
throw new RuntimeException("Unknown Sample Name: " + sample); throw new RuntimeException("Unknown Sample Name: " + sample);
} }
readNames.append(read.getReadName()).append("+").append(read.getAlignmentStart()).append("+").append(read.getCigarString());
} }
@ -129,9 +131,12 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
} }
lastPosition = context.getPosition(); lastPosition = context.getPosition();
if (extendedOutput) {
sb.append(context.getPosition()).append(" ");
}
sb.append((isTumorCovered && isNormalCovered)?"1":"0"); sb.append((isTumorCovered && isNormalCovered)?"1":"0");
if (extendedOutput) { if (extendedOutput) {
sb.append(" ").append(tumorDepth).append(" ").append(normalDepth); sb.append(" ").append(tumorDepth).append(" ").append(normalDepth).append(" ").append(readNames);
} }
// sb.append(context.getContig()).append(" "); // sb.append(context.getContig()).append(" ");