From 675ccab2fa73eb88023285cfc0f3130afbdd3406 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 23 Jul 2012 10:17:17 -0400 Subject: [PATCH] Renaming BQSR to BaseRecalibrator --- .../sting/gatk/walkers/bqsr/BQSRIntegrationTest.java | 4 ++-- .../gatk/walkers/bqsr/{BQSR.java => BaseRecalibrator.java} | 2 +- .../sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java | 2 +- .../sting/queue/qscripts/DataProcessingPipeline.scala | 2 +- .../sting/queue/qscripts/PacbioProcessingPipeline.scala | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) rename public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/{BQSR.java => BaseRecalibrator.java} (99%) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java index 635a74399..1d506b88c 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java @@ -59,7 +59,7 @@ public class BQSRIntegrationTest extends WalkerTest { @Test(dataProvider = "BQSRTest") public void testBQSR(BQSRTest params) { WalkerTestSpec spec = new WalkerTestSpec( - " -T BQSR" + + " -T BaseRecalibrator" + " -R " + params.reference + " -I " + params.bam + " -L " + params.interval + @@ -74,7 +74,7 @@ public class BQSRIntegrationTest extends WalkerTest { @Test public void testBQSRFailWithoutDBSNP() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - " -T BQSR" + + " -T BaseRecalibrator" + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam" + " -L 1:10,000,000-10,200,000" + diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java similarity index 99% rename from public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java rename to public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 1a03ce1ce..0b1f2c478 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSR.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -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 @PartitionBy(PartitionType.LOCUS) // this walker requires both -I input.bam and -R reference.fasta -public class BQSR extends LocusWalker implements TreeReducible { +public class BaseRecalibrator extends LocusWalker implements TreeReducible { @ArgumentCollection private final RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection(); // all the command line arguments for BQSR and it's covariates diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java index 55c04f1b7..a24506d07 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java @@ -105,6 +105,6 @@ public class StandardRecalibrationEngine implements RecalibrationEngine, PublicP * @return the covariate keysets for this read */ protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) { - return (ReadCovariates) read.getTemporaryAttribute(BQSR.COVARS_ATTRIBUTE); + return (ReadCovariates) read.getTemporaryAttribute(BaseRecalibrator.COVARS_ATTRIBUTE); } } diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala index 70c89ac31..56e2ddebb 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala @@ -343,7 +343,7 @@ class DataProcessingPipeline extends QScript { 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.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate") this.input_file :+= inBam diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala index 86f2d4969..b7246ca8f 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala @@ -160,7 +160,7 @@ class PacbioProcessingPipeline extends QScript { 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) this.DBQ = dbq this.knownSites :+= dbSNP