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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
This commit is contained in:
jmaguire 2009-12-18 00:52:48 +00:00
parent 8787dd4c5e
commit 98839193b7
1 changed files with 5 additions and 4 deletions
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9
java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java
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@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.*;
import edu.mit.broad.picard.util.Interval; import edu.mit.broad.picard.util.Interval;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.*; import java.io.*;
@ -172,7 +173,7 @@ class CheckRefFields extends CommandLineProgram
{ {
VCFRecord record = reader.next(); VCFRecord record = reader.next();
String chr = record.getChromosome(); String chr = record.getLocation().getContig();
if (! chr.equals(ref_seq_name)) if (! chr.equals(ref_seq_name))
{ {
System.out.println("Loading " + chr); System.out.println("Loading " + chr);
@ -180,7 +181,7 @@ class CheckRefFields extends CommandLineProgram
ref_seq_name = chr; ref_seq_name = chr;
} }
long offset = record.getPosition(); long offset = record.getLocation().getStart();
char vcf_ref_base = record.getReferenceBase(); char vcf_ref_base = record.getReferenceBase();
char fasta_ref_base = (char)ref_seq[(int)offset-1]; char fasta_ref_base = (char)ref_seq[(int)offset-1];
@ -246,7 +247,7 @@ class FixRefFields extends CommandLineProgram
{ {
VCFRecord record = reader.next(); VCFRecord record = reader.next();
String chr = record.getChromosome(); String chr = record.getLocation().getContig();
if (! chr.equals(ref_seq_name)) if (! chr.equals(ref_seq_name))
{ {
System.out.println("Loading " + chr); System.out.println("Loading " + chr);
@ -254,7 +255,7 @@ class FixRefFields extends CommandLineProgram
ref_seq_name = chr; ref_seq_name = chr;
} }
long offset = record.getPosition(); long offset = record.getLocation().getStart();
char vcf_ref_base = record.getReferenceBase(); char vcf_ref_base = record.getReferenceBase();
char fasta_ref_base = (char)ref_seq[(int)offset-1]; char fasta_ref_base = (char)ref_seq[(int)offset-1];