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

ivy.xml

@@ -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" />

java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java

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

java/src/org/broadinstitute/sting/gatk/LocusContext.java

@@ -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

java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java

@@ -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

java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java

@@ -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

java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java

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

java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java

@@ -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

java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java

@@ -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;

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -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;

java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java

@@ -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;
 
 /**

java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java

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

java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java

@@ -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;

java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java

@@ -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

java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java

@@ -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 net.sf.picard.reference.ReferenceSequenceFile;
-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>

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -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.*;
 

java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java

@@ -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>

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

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

java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java

@@ -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 net.sf.picard.filter.FilteringIterator;
-import edu.mit.broad.picard.filter.SamRecordFilter;
+import net.sf.picard.filter.SamRecordFilter;
 
 /**
  *

java/src/org/broadinstitute/sting/playground/ValidateSAM.java

@@ -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 net.sf.picard.cmdline.CommandLineProgram;
-import edu.mit.broad.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Usage;
-import edu.mit.broad.picard.cmdline.Option;
+import net.sf.picard.cmdline.Option;
 
 import java.io.*;
 

java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java

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

java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java

@@ -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
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java

@@ -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> {
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java

@@ -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> {
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java

@@ -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;
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java

@@ -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;

java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java

@@ -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> {
 

java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java

@@ -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.*;

java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java

@@ -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 net.sf.picard.cmdline.CommandLineProgram;
-import edu.mit.broad.picard.cmdline.Option;
+import net.sf.picard.cmdline.Option;
-import edu.mit.broad.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Usage;
-import edu.mit.broad.picard.reference.ReferenceSequenceFileWalker;
+import net.sf.picard.reference.ReferenceSequenceFileWalker;
-import edu.mit.broad.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequence;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.GenomeLoc;

java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java

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

java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java

@@ -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;
 

java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java

@@ -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();

java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -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;

java/src/org/broadinstitute/sting/utils/Utils.java

@@ -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;

java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java

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

java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java

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

java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java

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

java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java

@@ -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

java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java

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

java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java

@@ -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

java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java

@@ -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.*;

java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java

@@ -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;

java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java

@@ -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 net.sf.picard.reference.ReferenceSequence;
-import edu.mit.broad.picard.PicardException;
+import net.sf.picard.PicardException;
 import net.sf.samtools.util.StringUtil;
 
 /**

settings/repository/edu.mit.broad/picard-200903262219.xml

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

settings/repository/edu.mit.broad/picard-private-771.xml

@@ -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>

settings/repository/net.sf/picard-1.01.26.xml

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

settings/repository/net.sf/sam-1.0.10.xml

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

settings/repository/net.sf/sam-1.0.26.xml

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