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clean up from VQSR movement 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5741 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-03 20:35:30 +00:00
parent 23cd3a7a5d
commit b88dec387c
2 changed files with 3 additions and 3 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -41,7 +41,7 @@ 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.gatk.walkers.RMD; import org.broadinstitute.sting.gatk.walkers.RMD;
import org.broadinstitute.sting.gatk.walkers.Requires; import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.playground.gatk.walkers.variantrecalibration.VQSRCalibrationCurve; import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibrationCurve;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.SampleUtils;

4
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -174,10 +174,10 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
// Add select expressions for anything in the tranches file // Add select expressions for anything in the tranches file
if ( TRANCHE_FILENAME != null ) { if ( TRANCHE_FILENAME != null ) {
// we are going to build a few select names automatically from the tranches file // we are going to build a few select names automatically from the tranches file
for ( Tranche t : Tranche.readTraches(new File(TRANCHE_FILENAME)) ) { for ( Tranche t : Tranche.readTranches(new File(TRANCHE_FILENAME)) ) {
logger.info("Adding select for all variant above the pCut of : " + t); logger.info("Adding select for all variant above the pCut of : " + t);
SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod)); SELECT_EXPS.add(String.format(VariantRecalibrator.VQS_LOD_KEY + " >= %.2f", t.minVQSLod));
SELECT_NAMES.add(String.format("FDR-%.2f", t.fdr)); SELECT_NAMES.add(String.format("TS-%.2f", t.ts));
} }
} }