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); /*