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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-07-23 11:28:26 -04:00
parent 10d143c35c 675ccab2fa
commit 2a14bbe4f0
5 changed files with 6 additions and 6 deletions
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4
protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
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@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest {
@Test(dataProvider = "BQSRTest") @Test(dataProvider = "BQSRTest")
public void testBQSR(BQSRTest params) { public void testBQSR(BQSRTest params) {
WalkerTestSpec spec = new WalkerTestSpec( WalkerTestSpec spec = new WalkerTestSpec(
" -T BQSR" + " -T BaseRecalibrator" +
" -R " + params.reference + " -R " + params.reference +
" -I " + params.bam + " -I " + params.bam +
" -L " + params.interval + " -L " + params.interval +
@ -74,7 +74,7 @@ public class BQSRIntegrationTest extends WalkerTest {
@Test @Test
public void testBQSRFailWithoutDBSNP() { public void testBQSRFailWithoutDBSNP() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
" -T BQSR" + " -T BaseRecalibrator" +
" -R " + b36KGReference + " -R " + b36KGReference +
" -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" + " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" +
" -L 1:10,000,000-10,200,000" + " -L 1:10,000,000-10,200,000" +

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java → public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
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@ -106,7 +106,7 @@ import java.util.ArrayList;
@Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality @Requires({DataSource.READS, DataSource.REFERENCE, DataSource.REFERENCE_BASES}) // filter out all reads with zero or unavailable mapping quality
@PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta
public class BQSR extends LocusWalker<Long, Long> implements TreeReducible<Long> { public class BaseRecalibrator extends LocusWalker<Long, Long> implements TreeReducible<Long> {
@ArgumentCollection @ArgumentCollection
private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates

2
public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java
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@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP
* @return the covariate keysets for this read * @return the covariate keysets for this read
*/ */
protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) { protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE); return (ReadCovariates) read.getTemporaryAttribute(BaseRecalibrator.COVARS_ATTRIBUTE);
} }
} }

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -343,7 +343,7 @@ class DataProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".clean" this.jobName = queueLogDir + outBam + ".clean"
} }
case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File) extends BaseRecalibrator with CommandLineGATKArgs {
this.knownSites ++= qscript.dbSNP this.knownSites ++= qscript.dbSNP
this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam this.input_file :+= inBam

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -160,7 +160,7 @@ class PacbioProcessingPipeline extends QScript {
this.jobName = queueLogDir + outBam + ".rg" this.jobName = queueLogDir + outBam + ".rg"
} }
case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File, resetQuals: Boolean) extends BaseRecalibrator with CommandLineGATKArgs {
if (resetQuals) if (resetQuals)
this.DBQ = dbq this.DBQ = dbq
this.knownSites :+= dbSNP this.knownSites :+= dbSNP