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* fixed (with Matt's help) the argument parsing 

* outputting UCSC wiggle format

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@422 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-15 02:17:39 +00:00
parent 24722a442e
commit d4aaa1bef4
1 changed files with 30 additions and 6 deletions
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36
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
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@ -19,13 +19,15 @@ import edu.mit.broad.picard.PicardException;
public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> { public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName = "tumor_sample_name", shortName = "1", required = true) @Argument(fullName = "tumor_sample_name", shortName = "s1", required = true)
String tumorSampleName = "TCGA-06-0188-01A-01W"; // FIXME: cmdline parsing not working! public String tumorSampleName;
@Argument(fullName = "normal_sample_name", shortName = "2", required = true) @Argument(fullName = "normal_sample_name", shortName = "s2", required = true)
String normalSampleName = "TCGA-06-0188-10B-01W"; // FIXME: cmdline parsing not working! public String normalSampleName;
// --normal_sample_name TCGA-06-0188-10B-01W --tumor_sample_name TCGA-06-0188-01A-01W
public void initialize() { public void initialize() {
out.println("track type=wiggle_0 name=SomaticCoverage viewLimits=0:1 graphType=heatmap");
} }
public String walkerType() { return "ByLocus"; } public String walkerType() { return "ByLocus"; }
@ -45,6 +47,9 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
int somaticCovered; int somaticCovered;
long start = 0; long start = 0;
int lastContigIndex = -1;
long lastPosition = -1;
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
if (start ==0) { start = System.currentTimeMillis(); } if (start ==0) { start = System.currentTimeMillis(); }
@ -97,9 +102,28 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
// out.println(String.format("%s:%d %d %d %d %d %dms", context.getContig(), context.getPosition(), totalSites, tumorCovered, normalCovered, somaticCovered, (now-start))); // out.println(String.format("%s:%d %d %d %d %d %dms", context.getContig(), context.getPosition(), totalSites, tumorCovered, normalCovered, somaticCovered, (now-start)));
// } // }
// if the contig index has changed OR if it's the same contig index but we jumped positions
// output a wiggle header
StringBuilder sb = new StringBuilder(); StringBuilder sb = new StringBuilder();
sb.append(context.getContig()).append(" "); if (lastContigIndex != context.getLocation().getContigIndex() ||
sb.append(context.getPosition()); lastPosition + 1 != context.getPosition()) {
lastContigIndex = context.getLocation().getContigIndex();
sb.append("fixedStep\t")
.append("chrom=").append(context.getContig()).append("\t")
.append("start=").append(context.getPosition()).append("\t")
.append("step=1")
.append("\n");
}
lastPosition = context.getPosition();
sb.append((isTumorCovered && isNormalCovered)?"1":"0");
// sb.append(context.getContig()).append(" ");
// sb.append(context.getPosition()).append(" ");
// sb.append(tumorDepth).append(" ");
// sb.append(normalDepth).append(" ");
// sb.append((isTumorCovered && isNormalCovered)?"Y":"N");
out.println(sb.toString()); out.println(sb.toString());
return 1; return 1;
} }