diff --git a/ivy.xml b/ivy.xml
index bcfa9d326..05f40e2e3 100644
--- a/ivy.xml
+++ b/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" />
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 9ba375483..eb2651956 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/gatk/LocusContext.java b/java/src/org/broadinstitute/sting/gatk/LocusContext.java
index 72e8dd1bb..d98fa70a4 100755
--- a/java/src/org/broadinstitute/sting/gatk/LocusContext.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java
index 6827bb66e..ee7cd7d21 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/CoveredLocusView.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java
index 0c0388eb9..f32879b53 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceView.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java
index b34f28714..456a45576 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/LocusView.java
+++ b/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 edu.mit.broad.picard.filter.SamRecordFilter;
+import net.sf.picard.filter.FilteringIterator;
+import net.sf.picard.filter.SamRecordFilter;
 /**
  * User: hanna
  * Date: May 13, 2009
diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java b/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java
index e7e27fdef..172e1767b 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceView.java
+++ b/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
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 5571028a3..0f7b19743 100755
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMDataSource.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
index c85bff529..3eee8c22b 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
index dcb23bcb0..a3ee99b2f 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
+++ b/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;
 
 /**
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java b/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
index fb238b55a..0e9d4cafc 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
index 6b381e1f8..20fb3a8c7 100755
--- a/java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java
index 443b90b7e..bed1ac766 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java
+++ b/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
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java b/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
index 737649c34..1f3088a26 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java
+++ b/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 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>
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 9b0739c74..57255a25e 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/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.*;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
index 52ac3b2e8..b2da4b22f 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java
+++ b/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>
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
index 59e2082fb..f149ec22b 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
index 109c9269a..25c033806 100755
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseDuplicates.java
+++ b/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 edu.mit.broad.picard.filter.SamRecordFilter;
+import net.sf.picard.filter.FilteringIterator;
+import net.sf.picard.filter.SamRecordFilter;
 
 /**
  *
diff --git a/java/src/org/broadinstitute/sting/playground/ValidateSAM.java b/java/src/org/broadinstitute/sting/playground/ValidateSAM.java
index 1f9230f02..9b5b91531 100755
--- a/java/src/org/broadinstitute/sting/playground/ValidateSAM.java
+++ b/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 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.*;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java b/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
index 36d09f35a..ba5e69d91 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java
+++ b/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 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.*;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java
index a14facd4a..15ba86991 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
index 860c94a7c..67bdda7cf 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
+++ b/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
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
index 54e3ef7a6..02dfcb3c2 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchCounterWalker.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
index 8874a0f36..317f63015 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MismatchHistoWalker.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java
index a5b6b2d4f..ada637fa5 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Pilot3CoverageWalker.java
+++ b/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> {
 
@@ -130,4 +130,4 @@ public class Pilot3CoverageWalker extends LocusWalker<Integer, Integer> {
 
 
 
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
index ec631066b..a5517b380 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/PopPriorWalker.java
+++ b/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> {
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
index c6d5e4cd3..eb4bb0303 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadErrorRateWalker.java
+++ b/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;
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java
index 5a95e2a9a..7f8c368ac 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReplaceQuals.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
index 81ef7ac89..329641316 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SomaticCoverageWalker.java
+++ b/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> {
 
@@ -164,4 +164,4 @@ public class SomaticCoverageWalker extends LocusWalker<Integer, Integer> {
 
 
 
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java b/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
index 6c30e5f41..dcf25b03f 100644
--- a/java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
+++ b/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.*;
diff --git a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java b/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
index 283031499..48a81a5a4 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java b/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java
index 184168a79..afef06875 100755
--- a/java/src/org/broadinstitute/sting/playground/indels/ShowMSA.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java b/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
index 1a5d58140..e80319076 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/WhitespaceTextFileParser.java
@@ -40,4 +40,4 @@ public class WhitespaceTextFileParser extends BasicTextFileParser {
     protected boolean isDelimiter(byte b) {
         return Character.isWhitespace((char)b);
     }
-}
\ No newline at end of file
+}
diff --git a/java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java b/java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java
index 9bece319d..856bc1a05 100644
--- a/java/src/org/broadinstitute/sting/secondarybase/FirecrestFileParser.java
+++ b/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;
 
diff --git a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java b/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
index 03f7be477..453f35510 100644
--- a/java/src/org/broadinstitute/sting/secondarybase/FourBaseRecaller.java
+++ b/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();
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index bcdc6f038..3f4e97b1e 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index 615c9cacd..7bccfafff 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/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;
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
index bf6bc6d36..d73267ef5 100644
--- a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
+++ b/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 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.*;
 
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
index 79c982999..80643e06d 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
+++ b/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 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;
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
index 8f222b9be..026a60cfc 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
+++ b/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 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;
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java
index 58c5c92c9..1f33702ee 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusReferenceViewTest.java
+++ b/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
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java b/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java
index b7206aed3..042fd030c 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/LocusViewTemplate.java
+++ b/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 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;
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java
index b01249565..aafca4350 100755
--- a/java/test/org/broadinstitute/sting/gatk/dataSources/providers/ReadReferenceViewTest.java
+++ b/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
diff --git a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
index bf2950167..682ba6772 100755
--- a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
+++ b/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.*;
diff --git a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
index c3853424e..397d0657b 100755
--- a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
+++ b/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;
diff --git a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java b/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
index 265f02ebd..84b8f14d3 100755
--- a/java/test/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFileTest.java
+++ b/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 edu.mit.broad.picard.PicardException;
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.PicardException;
 import net.sf.samtools.util.StringUtil;
 
 /**
diff --git a/settings/repository/edu.mit.broad/picard-200903262219.jar b/settings/repository/edu.mit.broad/picard-200903262219.jar
deleted file mode 100644
index 1f8d6e7ce..000000000
Binary files a/settings/repository/edu.mit.broad/picard-200903262219.jar and /dev/null differ
diff --git a/settings/repository/edu.mit.broad/picard-200903262219.xml b/settings/repository/edu.mit.broad/picard-200903262219.xml
deleted file mode 100644
index 165b503ef..000000000
--- a/settings/repository/edu.mit.broad/picard-200903262219.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard" revision="200903262219" status="integration" publication="20090326221900" />
-</ivy-module>
diff --git a/settings/repository/edu.mit.broad/picard-private-771.jar b/settings/repository/edu.mit.broad/picard-private-771.jar
new file mode 100644
index 000000000..07f7262bd
Binary files /dev/null and b/settings/repository/edu.mit.broad/picard-private-771.jar differ
diff --git a/settings/repository/edu.mit.broad/picard-private-771.xml b/settings/repository/edu.mit.broad/picard-private-771.xml
new file mode 100644
index 000000000..9120743dc
--- /dev/null
+++ b/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>
diff --git a/settings/repository/net.sf/picard-1.01.26.jar b/settings/repository/net.sf/picard-1.01.26.jar
new file mode 100644
index 000000000..c03d34295
Binary files /dev/null and b/settings/repository/net.sf/picard-1.01.26.jar differ
diff --git a/settings/repository/net.sf/picard-1.01.26.xml b/settings/repository/net.sf/picard-1.01.26.xml
new file mode 100644
index 000000000..4edbe7050
--- /dev/null
+++ b/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>
diff --git a/settings/repository/net.sf/sam-1.0.10.xml b/settings/repository/net.sf/sam-1.0.10.xml
deleted file mode 100644
index b97ba7e6e..000000000
--- a/settings/repository/net.sf/sam-1.0.10.xml
+++ /dev/null
@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.0.10" status="release" />
-</ivy-module>
diff --git a/settings/repository/net.sf/sam-1.0.10.jar b/settings/repository/net.sf/sam-1.0.26.jar
similarity index 90%
rename from settings/repository/net.sf/sam-1.0.10.jar
rename to settings/repository/net.sf/sam-1.0.26.jar
index 9c0f13413..93f1ebbdd 100644
Binary files a/settings/repository/net.sf/sam-1.0.10.jar and b/settings/repository/net.sf/sam-1.0.26.jar differ
diff --git a/settings/repository/net.sf/sam-1.0.26.xml b/settings/repository/net.sf/sam-1.0.26.xml
new file mode 100644
index 000000000..c0d9b102b
--- /dev/null
+++ b/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>