zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-05-28 20:13:01 +00:00
parent 19f9ac2b05
commit 5e8c08ee63
55 changed files with 103 additions and 90 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
ivy.xml
View File

@ -2,7 +2,8 @@
<info organisation="org.broadinstitute" module="Sting"/>
<dependencies>
<dependency org="net.sf" name="sam" rev="latest.integration" />
<dependency org="edu.mit.broad" name="picard" rev="latest.integration" />
<dependency org="net.sf" name="picard" rev="latest.integration" />
<dependency org="edu.mit.broad" name="picard-private" rev="latest.integration" />
<dependency org="junit" name="junit" rev="4.4" />
<dependency org="log4j" name="log4j" rev="1.2.15" />
<dependency org="colt" name="colt" rev="1.2.0" />

4
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import org.apache.log4j.Logger;

2
java/src/org/broadinstitute/sting/gatk/LocusContext.java
View File

@ -9,7 +9,7 @@ import java.util.TreeSet;
import java.util.Random;
import org.broadinstitute.sting.utils.GenomeLoc;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
/**
* Useful class for forwarding on locusContext data from this iterator

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java
View File

@ -13,7 +13,7 @@ import net.sf.samtools.SAMRecord;
import java.util.ArrayList;
import java.util.Iterator;
import edu.mit.broad.picard.filter.FilteringIterator;
import net.sf.picard.filter.FilteringIterator;
/**
* User: hanna
* Date: May 12, 2009

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.dataSources.providers;
import org.broadinstitute.sting.utils.GenomeLoc;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
/**
* User: hanna

4
java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java
View File

@ -15,8 +15,8 @@ import java.util.Collection;
import java.util.Collections;
import java.util.Arrays;
import edu.mit.broad.picard.filter.FilteringIterator;
import edu.mit.broad.picard.filter.SamRecordFilter;
import net.sf.picard.filter.FilteringIterator;
import net.sf.picard.filter.SamRecordFilter;
/**
* User: hanna
* Date: May 13, 2009

2
java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.dataSources.providers;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.StringUtil;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
/**
* User: hanna
* Date: May 22, 2009

2
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
import edu.mit.broad.picard.sam.SamFileHeaderMerger;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;

2
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.executive;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFile;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;

2
java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.util.Iterator;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
/**

8
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
View File

@ -10,10 +10,10 @@
*/
package org.broadinstitute.sting.gatk.iterators;
import edu.mit.broad.picard.PicardException;
import edu.mit.broad.picard.sam.ReservedTagConstants;
import edu.mit.broad.picard.sam.SamFileHeaderMerger;
import edu.mit.broad.picard.util.PeekableIterator;
import net.sf.picard.PicardException;
import net.sf.picard.sam.ReservedTagConstants;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.picard.util.PeekableIterator;
import net.sf.samtools.*;
import net.sf.samtools.util.CloseableIterator;
import org.apache.log4j.Logger;

2
java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.iterators;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.RuntimeIOException;
import net.sf.samtools.util.StringUtil;
import org.apache.log4j.Logger;

2
java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.Utils;
import java.util.List;
import java.util.Arrays;
import edu.mit.broad.picard.util.SequenceUtil;
import net.sf.picard.util.SequenceUtil;
/**
* ReferenceOrderedDatum class to hold HapMap AlleleFrequency Data

4
java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
View File

@ -13,8 +13,8 @@ import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.Pileup;
import org.broadinstitute.sting.utils.xReadLines;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFileWalker;
/**
* This class wraps Maq/samtools allele calls from pileup format and presents them as a ROD.<br>

2
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.gatk.refdata;
import edu.mit.broad.picard.util.SequenceUtil;
import net.sf.picard.util.SequenceUtil;
import java.util.*;

2
java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
View File

@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
import net.sf.picard.reference.ReferenceSequenceFileWalker;
/**
* This class wraps Maq/samtools allele calls from pileup format and presents them as a ROD.<br>

6
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.traversals;
import edu.mit.broad.picard.filter.SamRecordFilter;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.sam.SamFileHeaderMerger;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileReader.ValidationStringency;

4
java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
View File

@ -18,8 +18,8 @@ import org.broadinstitute.sting.utils.Pair;
import java.io.File;
import java.util.*;
import edu.mit.broad.picard.filter.FilteringIterator;
import edu.mit.broad.picard.filter.SamRecordFilter;
import net.sf.picard.filter.FilteringIterator;
import net.sf.picard.filter.SamRecordFilter;
/**
*

6
java/src/org/broadinstitute/sting/playground/ValidateSAM.java
View File

@ -3,9 +3,9 @@ package org.broadinstitute.sting.playground;
import net.sf.samtools.*;
import net.sf.samtools.SAMFileReader.ValidationStringency;
import net.sf.samtools.util.CloseableIterator;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.cmdline.Option;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import java.io.*;

10
java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
View File

@ -1,11 +1,11 @@
package org.broadinstitute.sting.playground.gatk;
import net.sf.samtools.SAMSequenceRecord;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.cmdline.Option;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.reference.ReferenceSequenceFile;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.gatk.refdata.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java
View File

@ -8,7 +8,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileWriter;
import net.sf.samtools.SAMFileWriterFactory;
import net.sf.samtools.SAMFileHeader;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import java.util.ArrayList;
import java.util.Random;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
View File

@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.playground.indels.*;
import net.sf.samtools.*;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
// Investigates indels called in the alignment data

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
View File

@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.Utils;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import java.util.ArrayList;
import java.util.Arrays;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
View File

@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.utils.Utils;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import java.util.Iterator;
import java.util.List;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java
View File

@ -17,7 +17,7 @@ import java.util.Formatter;
import static java.lang.Math.log10;
import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.PicardException;
public class Pilot3CoverageWalker extends LocusWalker<Integer, Integer> {
@ -130,4 +130,4 @@ public class Pilot3CoverageWalker extends LocusWalker<Integer, Integer> {
}
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
View File

@ -15,7 +15,7 @@ import java.util.Formatter;
import static java.lang.Math.log10;
import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.PicardException;
public class PopPriorWalker extends LocusWalker<Integer, Integer> {

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.BaseUtils;
import net.sf.samtools.SAMRecord;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import java.util.Random;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java
View File

@ -6,7 +6,7 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Pair;
import net.sf.samtools.*;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import java.util.ArrayList;
import java.util.Random;

4
java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
View File

@ -17,7 +17,7 @@ import java.util.Formatter;
import static java.lang.Math.log10;
import edu.mit.broad.picard.genotype.DiploidGenotype;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.PicardException;
public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
@ -164,4 +164,4 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
}
}

2
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
View File

@ -3,7 +3,7 @@ package org.broadinstitute.sting.playground.indels;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import org.broadinstitute.sting.playground.utils.CountedObject;
import java.util.*;

10
java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
View File

@ -8,11 +8,11 @@ import java.util.HashMap;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileNameExtensionFilter;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.cmdline.Usage;
import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Option;
import net.sf.picard.cmdline.Usage;
import net.sf.picard.reference.ReferenceSequenceFileWalker;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.*;
import org.broadinstitute.sting.utils.GenomeLoc;

10
java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java
View File

@ -2,11 +2,11 @@ package org.broadinstitute.sting.playground.indels;
import java.io.File;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
import edu.mit.broad.picard.cmdline.CommandLineProgram;
import edu.mit.broad.picard.cmdline.Option;
import edu.mit.broad.picard.cmdline.Usage;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.reference.ReferenceSequenceFileWalker;
import net.sf.picard.cmdline.CommandLineProgram;
import net.sf.picard.cmdline.Option;
import net.sf.picard.cmdline.Usage;
import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.SAMFileReader;

2
java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
View File

@ -40,4 +40,4 @@ public class WhitespaceTextFileParser extends BasicTextFileParser {
protected boolean isDelimiter(byte b) {
return Character.isWhitespace((char)b);
}
}
}

4
java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java
View File

@ -9,9 +9,9 @@
*/
package org.broadinstitute.sting.secondarybase;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.PicardException;
import edu.mit.broad.picard.util.BasicTextFileParser;
import edu.mit.broad.picard.util.FormatUtil;
import net.sf.picard.util.FormatUtil;
import java.io.File;

15
java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
View File

@ -39,6 +39,15 @@ public class FourBaseRecaller extends CommandLineProgram {
@Argument(fullName="old", shortName="1", doc="Old Bustard 1.1 mode?", required=false)
public Boolean OLD = false;
@Argument(fullName="parse_sig2", shortName="P", doc="Parse sig2 files for Bustard pre-1.1 files (pre-1.1 only)")
public Boolean PARSE_SIG2_FILES = false;
@Argument(fullName="barcode", shortName="BCODE", doc="Only process reads that match this barcode (pre-1.1 only)")
public String BARCODE = null;
@Argument(fullName="barcode_cycle", shortName="BCYCLE", doc="1-based cycle number where barcode starts (pre-1.1 only)")
public Integer BARCODE_CYCLE = null;
@Argument(fullName="first_read_length", shortName="F", doc="First read length (v1.1 only)")
public Integer FIRST_READ_LENGTH;
public static void main(String[] argv) {
Instance = new FourBaseRecaller();
start(Instance, argv);
@ -62,7 +71,7 @@ public class FourBaseRecaller extends CommandLineProgram {
FirecrestFileParser ffp;
FirecrestReadData fread;
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE);
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
bread = bfp.next();
ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
fread = ffp.next();
@ -103,7 +112,7 @@ public class FourBaseRecaller extends CommandLineProgram {
// learn covariance parameters
System.err.println("Computing covariance parameters...");
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE);
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
bread = bfp.next();
ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
fread = ffp.next();
@ -141,7 +150,7 @@ public class FourBaseRecaller extends CommandLineProgram {
SAMFileHeader sfh = new SAMFileHeader();
SAMFileWriter sfw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sfh, false, OUT);
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE);
bfp = OLD ? new BustardFileParser_1_1(DIR, LANE, isPaired, RUN_BARCODE, FIRST_READ_LENGTH) : new BustardFileParser(DIR, LANE, isPaired, RUN_BARCODE, PARSE_SIG2_FILES, BARCODE, BARCODE_CYCLE);
bread = bfp.next();
ffp = new FirecrestFileParser(DIR.getParentFile(), LANE);
fread = ffp.next();

4
java/src/org/broadinstitute/sting/utils/GenomeLoc.java
View File

@ -1,8 +1,8 @@
package org.broadinstitute.sting.utils;
import edu.mit.broad.picard.directed.IntervalList;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.util.Interval;
import edu.mit.broad.picard.directed.IntervalList;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;

2
java/src/org/broadinstitute/sting/utils/Utils.java
View File

@ -4,7 +4,7 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.util.StringUtil;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFile;
import java.util.*;
import java.io.File;

8
java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
View File

@ -1,9 +1,9 @@
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.PicardException;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.io.IoUtil;
import net.sf.picard.PicardException;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.io.IoUtil;
import java.io.*;

4
java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
View File

@ -1,7 +1,7 @@
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.PicardException;
import edu.mit.broad.picard.io.IoUtil;
import net.sf.picard.PicardException;
import net.sf.picard.io.IoUtil;
import java.util.Scanner;
import java.util.Map;

8
java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
View File

@ -1,9 +1,9 @@
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.PicardException;
import edu.mit.broad.picard.io.IoUtil;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.PicardException;
import net.sf.picard.io.IoUtil;
import java.io.File;
import java.io.FileInputStream;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java
View File

@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.shards.LocusShard;
import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
/**
* User: hanna

4
java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java
View File

@ -17,8 +17,8 @@ import java.util.Iterator;
import java.util.ArrayList;
import java.util.Arrays;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMRecord;

2
java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java
View File

@ -9,7 +9,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.util.StringUtil;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
/**
* User: hanna
* Date: May 27, 2009

2
java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;
import org.broadinstitute.sting.BaseTest;
import org.junit.*;

2
java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
View File

@ -1,6 +1,6 @@
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.PicardException;
import org.broadinstitute.sting.BaseTest;
import org.junit.Assert;
import org.junit.Before;

4
java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
View File

@ -9,8 +9,8 @@ import org.broadinstitute.sting.BaseTest;
import java.io.File;
import java.io.FileNotFoundException;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.PicardException;
import net.sf.picard.reference.ReferenceSequence;
import net.sf.picard.PicardException;
import net.sf.samtools.util.StringUtil;
/**

BIN
settings/repository/edu.mit.broad/picard-200903262219.jar
View File

Binary file not shown.

3
settings/repository/edu.mit.broad/picard-200903262219.xml
View File

@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard" revision="200903262219" status="integration" publication="20090326221900" />
</ivy-module>

BIN
settings/repository/edu.mit.broad/picard-private-771.jar 100644
View File

Binary file not shown.

3
settings/repository/edu.mit.broad/picard-private-771.xml 100644
View File

@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private" revision="771" status="integration" publication="20090528143800" />
</ivy-module>

BIN
settings/repository/net.sf/picard-1.01.26.jar 100644
View File

Binary file not shown.

3
settings/repository/net.sf/picard-1.01.26.xml 100644
View File

@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.01.26" status="release" />
</ivy-module>

3
settings/repository/net.sf/sam-1.0.10.xml
View File

@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.0.10" status="release" />
</ivy-module>

BIN
settings/repository/net.sf/sam-1.0.10.jar → settings/repository/net.sf/sam-1.0.26.jar
View File

Binary file not shown.

3
settings/repository/net.sf/sam-1.0.26.xml 100644
View File

@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.0.26" status="release" />
</ivy-module>