From 5d2c2bd28036adb174534508a3de3783a673fa41 Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 6 Dec 2010 17:43:43 +0000 Subject: [PATCH] Just refactoring into utils/baq directory git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a --- java/src/org/broadinstitute/sting/gatk/ReadProperties.java | 2 +- .../sting/gatk/arguments/GATKArgumentCollection.java | 2 +- .../gatk/datasources/simpleDataSources/SAMDataSource.java | 3 ++- .../sting/gatk/walkers/qc/ValidateBAQWalker.java | 2 +- java/src/org/broadinstitute/sting/utils/{ => baq}/BAQ.java | 2 +- .../sting/{gatk/iterators => utils/baq}/BAQSamIterator.java | 5 +++-- .../sting/gatk/iterators/LocusIteratorByStateUnitTest.java | 2 +- 7 files changed, 10 insertions(+), 8 deletions(-) rename java/src/org/broadinstitute/sting/utils/{ => baq}/BAQ.java (99%) rename java/src/org/broadinstitute/sting/{gatk/iterators => utils/baq}/BAQSamIterator.java (89%) diff --git a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java index 3ac0ce429..b93b88152 100755 --- a/java/src/org/broadinstitute/sting/gatk/ReadProperties.java +++ b/java/src/org/broadinstitute/sting/gatk/ReadProperties.java @@ -6,7 +6,7 @@ import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileReader; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; import java.util.List; import java.util.Collection; diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index 7de4c0154..6ee58b862 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -34,7 +34,7 @@ import org.broadinstitute.sting.commandline.Input; import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.DownsamplingMethod; import org.broadinstitute.sting.utils.interval.IntervalSetRule; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; import org.simpleframework.xml.*; import org.simpleframework.xml.core.Persister; import org.simpleframework.xml.stream.Format; diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index c32c4661d..9b428f23f 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -44,7 +44,8 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.utils.baq.BAQSamIterator; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java index 7486eda1b..458a0097e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.utils.exceptions.StingException; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Argument; diff --git a/java/src/org/broadinstitute/sting/utils/BAQ.java b/java/src/org/broadinstitute/sting/utils/baq/BAQ.java similarity index 99% rename from java/src/org/broadinstitute/sting/utils/BAQ.java rename to java/src/org/broadinstitute/sting/utils/baq/BAQ.java index 6d49ef291..86a9f7b08 100644 --- a/java/src/org/broadinstitute/sting/utils/BAQ.java +++ b/java/src/org/broadinstitute/sting/utils/baq/BAQ.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils; +package org.broadinstitute.sting.utils.baq; import net.sf.samtools.SAMRecord; import net.sf.samtools.CigarElement; diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java similarity index 89% rename from java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java rename to java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java index 4095cae20..7fff240f2 100644 --- a/java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java +++ b/java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java @@ -1,8 +1,9 @@ -package org.broadinstitute.sting.gatk.iterators; +package org.broadinstitute.sting.utils.baq; import net.sf.samtools.SAMRecord; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; +import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import java.util.Iterator; diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java index 64efe19b2..e61d6f836 100644 --- a/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java @@ -13,7 +13,7 @@ import org.broadinstitute.sting.gatk.datasources.sample.SampleDataSource; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.utils.GenomeLocParser; -import org.broadinstitute.sting.utils.BAQ; +import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;