From 5744a1d9687dee9194a796ba46f349cc5e98ae11 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Mon, 23 Nov 2009 20:10:12 +0000 Subject: [PATCH] The covariates don't care about SAMRecord's anymore - Cleaning up the import statements. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2126 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/recalibration/Covariate.java | 2 -- .../sting/gatk/walkers/recalibration/CycleCovariate.java | 3 --- .../sting/gatk/walkers/recalibration/DinucCovariate.java | 2 -- .../gatk/walkers/recalibration/MappingQualityCovariate.java | 2 -- .../sting/gatk/walkers/recalibration/MinimumNQSCovariate.java | 2 -- .../sting/gatk/walkers/recalibration/PositionCovariate.java | 3 --- .../gatk/walkers/recalibration/PrimerRoundCovariate.java | 4 ---- .../gatk/walkers/recalibration/QualityScoreCovariate.java | 2 -- .../sting/gatk/walkers/recalibration/ReadGroupCovariate.java | 2 -- 9 files changed, 22 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java index 86af70b21..a078aa42c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/Covariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java index 32c29a9d9..b14958f45 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java @@ -1,10 +1,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.Utils; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java index d9f3c5557..098988cd9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/DinucCovariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - import java.util.HashMap; import org.broadinstitute.sting.utils.BaseUtils; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java index 035709262..11a9ec28c 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MappingQualityCovariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java index 13bf5750c..c27cdafcd 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/MinimumNQSCovariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java index 451770af5..ef3349c80 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PositionCovariate.java @@ -1,8 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.Utils; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java index a1e033e03..dd71fc9c1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java @@ -1,9 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import org.broadinstitute.sting.utils.StingException; - -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java index 894688885..bd9569c11 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/QualityScoreCovariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute * diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java index 15cec3c1e..51095a30f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadGroupCovariate.java @@ -1,7 +1,5 @@ package org.broadinstitute.sting.gatk.walkers.recalibration; -import net.sf.samtools.SAMRecord; - /* * Copyright (c) 2009 The Broad Institute *