From 5abfc7d079bed1786415dc7f1b96d19bf55274d8 Mon Sep 17 00:00:00 2001 From: kiran Date: Tue, 21 Apr 2009 22:27:26 +0000 Subject: [PATCH] Added an argument ('extended' or 'ext') that outputs the four-base probs in a long format. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@485 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/PileupWalker.java | 24 +++++++------------ 1 file changed, 8 insertions(+), 16 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java index 383bfd936..2a74e61f1 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java @@ -24,6 +24,9 @@ import java.util.ArrayList; public class PileupWalker extends LocusWalker { @Argument(fullName="verbose",required=false,defaultValue="false") public boolean VERBOSE; + + @Argument(fullName="extended",shortName="ext",required=false,defaultValue="false") + public boolean EXTENDED; public boolean FLAG_UNCOVERED_BASES = true; // todo: how do I make this a command line argument? @@ -47,22 +50,6 @@ public class PileupWalker extends LocusWalker { if ( VERBOSE ) { extras += " BQ=" + pileup.getQualsAsInts(); extras += " MQ=" + pileup.getMappingQualsAsInts(); - - String sqbases = pileup.getSecondaryBasePileup(); - String sqquals = pileup.getSecondaryQualPileup(); - if (sqbases != null && sqquals != null) { - assert(sqbases.length() == sqquals.length()); - - extras += " SQ="; - for (int i = 0; i < sqbases.length(); i++) { - extras += sqbases.charAt(i); - extras += sqquals.charAt(i); - - if (i < sqbases.length() - 1) { - extras += ','; - } - } - } } String rodString = ""; @@ -85,6 +72,11 @@ public class PileupWalker extends LocusWalker { out.printf("%s%s %s%n", pileup.getPileupString(), extras, rodString); //} + if ( EXTENDED ) { + String probDists = pileup.getProbDistPileup(); + System.out.println(probDists); + } + return 1; }