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Somewhere along the way someone broke this tool and failed to update the documentation to boot. Fixing. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5705 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2011-04-28 03:16:20 +00:00
parent ae8f3f2cde
commit f34e6d5b8c
2 changed files with 11 additions and 8 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/CreateSequenomMask.java
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@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.RodWalker; import org.broadinstitute.sting.gatk.walkers.RodWalker;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.PrintStream; import java.io.PrintStream;
@ -25,7 +26,8 @@ public class CreateSequenomMask extends RodWalker<Integer, Integer> {
int result = 0; int result = 0;
for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) { for ( VariantContext vc : tracker.getAllVariantContexts(ref) ) {
if ( vc.isSNP() ) { if ( vc.isSNP() ) {
out.println(context.getLocation()); GenomeLoc loc = context.getLocation();
out.println(loc.getContig() + "\t" + (loc.getStart()-1) + "\t" + loc.getStop());
result = 1; result = 1;
break; break;
} }

15
java/src/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbes.java
View File

@ -26,6 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.sequenom; package org.broadinstitute.sting.gatk.walkers.sequenom;
import net.sf.samtools.util.CloseableIterator; import net.sf.samtools.util.CloseableIterator;
import org.broad.tribble.bed.BEDCodec;
import org.broad.tribble.dbsnp.DbSNPCodec; import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
@ -44,6 +45,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import java.io.File;
import java.util.*; import java.util.*;
import java.io.PrintStream; import java.io.PrintStream;
@ -88,19 +90,18 @@ public class PickSequenomProbes extends RodWalker<String, String> {
if ( SNP_MASK != null ) { if ( SNP_MASK != null ) {
logger.info("Loading SNP mask... "); logger.info("Loading SNP mask... ");
ReferenceOrderedData snp_mask; ReferenceOrderedData snp_mask;
if ( SNP_MASK.contains(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)) { //if ( SNP_MASK.contains(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME)) {
RMDTrackBuilder builder = new RMDTrackBuilder(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),getToolkit().getGenomeLocParser(),getToolkit().getArguments().unsafe); RMDTrackBuilder builder = new RMDTrackBuilder(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),getToolkit().getGenomeLocParser(),getToolkit().getArguments().unsafe);
RMDTrack track = builder.createInstanceOfTrack(DbSNPCodec.class,new java.io.File(SNP_MASK)); RMDTrack track = builder.createInstanceOfTrack(BEDCodec.class, new File(SNP_MASK));
snpMaskIterator = new SeekableRODIterator(track.getHeader(), snpMaskIterator = new SeekableRODIterator(track.getHeader(),
track.getSequenceDictionary(), track.getSequenceDictionary(),
getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(), getToolkit().getReferenceDataSource().getReference().getSequenceDictionary(),
getToolkit().getGenomeLocParser(), getToolkit().getGenomeLocParser(),
track.getIterator()); track.getIterator());
//} else {
} else { // // TODO: fix me when Plink is back
// TODO: fix me when Plink is back // throw new IllegalArgumentException("We currently do not support other snp_mask tracks (like Plink)");
throw new IllegalArgumentException("We currently do not support other snp_mask tracks (like Plink)"); //}
}
} }
VCs = new VariantCollection(); VCs = new VariantCollection();