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Minor improvements to indel genotyper: 

a) Ability to specify haplotype size from command line
b) Expand reference context  window so we can form haplotypes for longer indel events.
c) small bug fix in temp output writer (to be removed once I can emit vcfs)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4212 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2010-09-03 22:52:08 +00:00
parent 7eeabe534a
commit ef7454a241
1 changed files with 5 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java
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@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
import org.broadinstitute.sting.gatk.walkers.Window;
@Reference(window=@Window(start=-5,stop=50))
@Reference(window=@Window(start=-10,stop=80))
@Allows({DataSource.READS, DataSource.REFERENCE})
public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
@Output
@ -69,6 +69,9 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
double alphaDeletionProbability = 0.01;
@Argument(fullName="haplotypeSize",shortName="hsize",doc="Size of haplotypes to evaluate calls.",required=true)
int HAPLOTYPE_SIZE = 40;
@Override
@ -80,7 +83,6 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
private HaplotypeIndelErrorModel model;
private static final int HAPLOTYPE_SIZE = 20;
private static final int MAX_READ_LENGTH = 200; // TODO- make this dynamic
@ -196,7 +198,7 @@ public class SimpleIndelGenotyperWalker extends RefWalker<Integer,Integer> {
else
newG = "OTHER";
out.format("NewG %s OldG %s\n", oldG, newG);
out.format("NewG %s OldG %s\n", newG, oldG);
/*