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Just refactoring into utils/baq directory 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-12-06 17:43:43 +00:00
parent aec6c0a030
commit 5d2c2bd280
7 changed files with 10 additions and 8 deletions
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2
java/src/org/broadinstitute/sting/gatk/ReadProperties.java
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@ -6,7 +6,7 @@ import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileReader;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; 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.List;
import java.util.Collection; import java.util.Collection;

2
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -34,7 +34,7 @@ import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.DownsampleType; import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.DownsamplingMethod; import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.utils.interval.IntervalSetRule; 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.*;
import org.simpleframework.xml.core.Persister; import org.simpleframework.xml.core.Persister;
import org.simpleframework.xml.stream.Format; import org.simpleframework.xml.stream.Format;

3
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
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@ -44,7 +44,8 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator; import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; 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.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;

2
java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidateBAQWalker.java
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@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.exceptions.StingException; 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.utils.MathUtils;
import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Argument;

2
java/src/org/broadinstitute/sting/utils/BAQ.java → java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils; package org.broadinstitute.sting.utils.baq;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;

5
java/src/org/broadinstitute/sting/gatk/iterators/BAQSamIterator.java → java/src/org/broadinstitute/sting/utils/baq/BAQSamIterator.java
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@ -1,8 +1,9 @@
package org.broadinstitute.sting.gatk.iterators; package org.broadinstitute.sting.utils.baq;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.picard.reference.IndexedFastaSequenceFile; 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; import java.util.Iterator;

2
java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
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@ -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.datasources.simpleDataSources.SAMReaderID;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.utils.GenomeLocParser; 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.pileup.ReadBackedExtendedEventPileup;
import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;