From ef7454a241627f5fbb45af69d8c839675e6f55f0 Mon Sep 17 00:00:00 2001 From: delangel Date: Fri, 3 Sep 2010 22:52:08 +0000 Subject: [PATCH] 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 --- .../walkers/SimpleIndelGenotyperWalker.java | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java index c043c7137..c9287a6c1 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/SimpleIndelGenotyperWalker.java @@ -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 { @Output @@ -69,6 +69,9 @@ public class SimpleIndelGenotyperWalker extends RefWalker { 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 { 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 { else newG = "OTHER"; - out.format("NewG %s OldG %s\n", oldG, newG); + out.format("NewG %s OldG %s\n", newG, oldG); /*