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CountCovariates makes sure that it sees a rod type that it expects for use as a variant mask (accepted types are dbsnp, vcf, and bed) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4296 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-09-16 18:53:42 +00:00
parent c1720cc8f5
commit 2eb5d9b2d2
1 changed files with 11 additions and 3 deletions
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10
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
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@ -25,7 +25,10 @@
package org.broadinstitute.sting.gatk.walkers.recalibration; package org.broadinstitute.sting.gatk.walkers.recalibration;
import org.broad.tribble.bed.BEDCodec;
import org.broad.tribble.dbsnp.DbSNPCodec;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broad.tribble.vcf.VCFCodec;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -179,14 +182,18 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
System.exit( 0 ); // Early exit here because user requested it System.exit( 0 ); // Early exit here because user requested it
} }
// Warn the user if no dbSNP file was specified // Warn the user if no dbSNP file or other variant mask was specified
boolean foundDBSNP = false; boolean foundDBSNP = false;
for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) { for( ReferenceOrderedDataSource rod : this.getToolkit().getRodDataSources() ) {
if( rod != null ) { if( rod != null ) {
if( rod.getReferenceOrderedData().getType().equals(DbSNPCodec.class) ||
rod.getReferenceOrderedData().getType().equals(VCFCodec.class) ||
rod.getReferenceOrderedData().getType().equals(BEDCodec.class) ) {
foundDBSNP = true; foundDBSNP = true;
break; break;
} }
} }
}
if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) { if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation."); throw new UserException.CommandLineException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
} }
@ -381,6 +388,7 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
* adding one to the number of observations and potentially one to the number of mismatches * adding one to the number of observations and potentially one to the number of mismatches
* Lots of things are passed as parameters to this method as a strategy for optimizing the covariate.getValue calls * Lots of things are passed as parameters to this method as a strategy for optimizing the covariate.getValue calls
* because pulling things out of the SAMRecord is an expensive operation. * because pulling things out of the SAMRecord is an expensive operation.
* @param counter Data structure which holds the counted bases
* @param gatkRead The SAMRecord holding all the data for this read * @param gatkRead The SAMRecord holding all the data for this read
* @param offset The offset in the read for this locus * @param offset The offset in the read for this locus
* @param refBase The reference base at this locus * @param refBase The reference base at this locus