From 98839193b701813525e174a061b3a5306e23eaf8 Mon Sep 17 00:00:00 2001 From: jmaguire Date: Fri, 18 Dec 2009 00:52:48 +0000 Subject: [PATCH] compatibility with VCF lib's switch to GenomeLoc. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2397 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/playground/tools/vcf/VCFTool.java | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java index 5713fb5e7..bfa1ec058 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; import edu.mit.broad.picard.util.Interval; +import org.broadinstitute.sting.utils.GenomeLoc; import java.io.*; @@ -172,7 +173,7 @@ class CheckRefFields extends CommandLineProgram { VCFRecord record = reader.next(); - String chr = record.getChromosome(); + String chr = record.getLocation().getContig(); if (! chr.equals(ref_seq_name)) { System.out.println("Loading " + chr); @@ -180,7 +181,7 @@ class CheckRefFields extends CommandLineProgram ref_seq_name = chr; } - long offset = record.getPosition(); + long offset = record.getLocation().getStart(); char vcf_ref_base = record.getReferenceBase(); char fasta_ref_base = (char)ref_seq[(int)offset-1]; @@ -246,7 +247,7 @@ class FixRefFields extends CommandLineProgram { VCFRecord record = reader.next(); - String chr = record.getChromosome(); + String chr = record.getLocation().getContig(); if (! chr.equals(ref_seq_name)) { System.out.println("Loading " + chr); @@ -254,7 +255,7 @@ class FixRefFields extends CommandLineProgram ref_seq_name = chr; } - long offset = record.getPosition(); + long offset = record.getLocation().getStart(); char vcf_ref_base = record.getReferenceBase(); char fasta_ref_base = (char)ref_seq[(int)offset-1];