diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java index c47df9e95..23ee0fade 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java @@ -1,8 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.shards; -import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import net.sf.samtools.*; import net.sf.picard.filter.SamRecordFilter; import java.util.List; @@ -22,7 +20,7 @@ public interface BAMFormatAwareShard extends Shard { * Get the list of chunks delimiting this shard. * @return a list of chunks that contain data for this shard. */ - public Map> getChunks(); + public Map getFileSpans(); /** * Returns true if this shard is meant to buffer reads, rather diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java index 761a46de8..36db37d68 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java @@ -1,8 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.shards; -import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader; -import net.sf.samtools.SAMRecord; +import net.sf.samtools.*; import net.sf.picard.filter.SamRecordFilter; import java.util.*; @@ -28,7 +26,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware /** * The data backing the next chunks to deliver to the traversal engine. */ - private final Map> chunks; + private final Map fileSpans; /** * The reads making up this shard. @@ -46,9 +44,9 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware */ private final Shard.ShardType shardType; - public BlockDelimitedReadShard(Reads sourceInfo, Map> chunks, SamRecordFilter filter, Shard.ShardType shardType) { + public BlockDelimitedReadShard(Reads sourceInfo, Map fileSpans, SamRecordFilter filter, Shard.ShardType shardType) { this.sourceInfo = sourceInfo; - this.chunks = chunks; + this.fileSpans = fileSpans; this.filter = filter; this.shardType = shardType; } @@ -58,6 +56,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * than just holding pointers to their locations. * @return True if this shard can buffer reads. False otherwise. */ + @Override public boolean buffersReads() { return true; } @@ -66,6 +65,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * Returns true if the read buffer is currently full. * @return True if this shard's buffer is full (and the shard can buffer reads). */ + @Override public boolean isBufferEmpty() { return reads.size() == 0; } @@ -74,6 +74,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * Returns true if the read buffer is currently full. * @return True if this shard's buffer is full (and the shard can buffer reads). */ + @Override public boolean isBufferFull() { return reads.size() > BlockDelimitedReadShardStrategy.MAX_READS; } @@ -82,6 +83,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * Adds a read to the read buffer. * @param read Add a read to the internal shard buffer. */ + @Override public void addRead(SAMRecord read) { // DO NOT validate that the buffer is full. Paired read sharding will occasionally have to stuff another // read or two into the buffer. @@ -92,10 +94,12 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * Creates an iterator over reads stored in this shard's read cache. * @return */ + @Override public StingSAMIterator iterator() { return StingSAMIteratorAdapter.adapt(sourceInfo,reads.iterator()); } + @Override public SamRecordFilter getFilter() { return filter; } @@ -104,8 +108,9 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware * Get the list of chunks delimiting this shard. * @return a list of chunks that contain data for this shard. */ - public Map> getChunks() { - return Collections.unmodifiableMap(chunks); + @Override + public Map getFileSpans() { + return Collections.unmodifiableMap(fileSpans); } /** @@ -123,14 +128,11 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware @Override public String toString() { StringBuilder sb = new StringBuilder(); - for(Map.Entry> entry: chunks.entrySet()) { + for(Map.Entry entry: fileSpans.entrySet()) { sb.append(entry.getKey()); sb.append(": "); - for(Chunk chunk : entry.getValue()) { - sb.append(chunk); - sb.append(' '); - } - sb.append(';'); + sb.append(entry.getValue()); + sb.append(' '); } return sb.toString(); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java index 12feb4c74..d50923055 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java @@ -55,7 +55,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy { /** * Ending position of the last shard in the file. */ - private Map position; + private Map position; /** * Create a new read shard strategy, loading read shards from the given BAM file. @@ -103,26 +103,18 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy { } public void advance() { - Map> shardPosition = new HashMap>(); + Map shardPosition = new HashMap(); nextShard = null; SamRecordFilter filter = null; if(locations != null) { - Map> selectedReaders = new HashMap>(); + Map selectedReaders = new HashMap(); while(selectedReaders.size() == 0 && currentFilePointer != null) { - shardPosition = currentFilePointer.chunks; + shardPosition = currentFilePointer.fileSpans; for(SAMReaderID id: shardPosition.keySet()) { - List chunks = shardPosition.get(id); - List selectedChunks = new ArrayList(); - Chunk filePosition = position.get(id); - for(Chunk chunk: chunks) - if(filePosition.getChunkStart() <= chunk.getChunkStart()) - selectedChunks.add(chunk); - else if(filePosition.getChunkStart() > chunk.getChunkStart() && filePosition.getChunkStart() < chunk.getChunkEnd()) { - selectedChunks.add(new Chunk(filePosition.getChunkStart(),chunk.getChunkEnd())); - } - if(selectedChunks.size() > 0) - selectedReaders.put(id,selectedChunks); + BAMFileSpan fileSpans = shardPosition.get(id).removeBefore(position.get(id)); + if(!fileSpans.isEmpty()) + selectedReaders.put(id,fileSpans); } if(selectedReaders.size() > 0) { @@ -141,13 +133,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy { } } else { - // TODO: This level of processing should not be necessary. - shardPosition = new HashMap>(); - for(Map.Entry entry: position.entrySet()) - shardPosition.put(entry.getKey(),Collections.singletonList(entry.getValue())); - filter = null; - - BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),shardPosition,filter,Shard.ShardType.READ); + BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),position,filter,Shard.ShardType.READ); dataSource.fillShard(shard); nextShard = !shard.isBufferEmpty() ? shard : null; } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java index 35bd1b94c..5d7ff317a 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java @@ -4,9 +4,8 @@ import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; -import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMRecord; +import net.sf.samtools.BAMFileSpan; import net.sf.picard.filter.SamRecordFilter; import java.util.List; @@ -45,7 +44,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa /** * A list of the chunks associated with this shard. */ - private final Map> chunks; + private final Map fileSpans; /** * An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types. @@ -56,23 +55,24 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa /** * Create a new locus shard, divided by index. * @param intervals List of intervals to process. - * @param chunks Chunks associated with that interval. + * @param fileSpans File spans associated with that interval. * @param shardType Type of the shard; must be either LOCUS or LOCUS_INTERVAL. */ - IndexDelimitedLocusShard(List intervals, Map> chunks, ShardType shardType) { + IndexDelimitedLocusShard(List intervals, Map fileSpans, ShardType shardType) { super(intervals); - this.chunks = chunks; + this.fileSpans = fileSpans; if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL) throw new StingException("Attempted to create an IndexDelimitedLocusShard with invalid shard type: " + shardType); this.shardType = shardType; } /** - * Gets the chunks associated with this locus shard. - * @return A list of the chunks to use when retrieving locus data. + * Gets the file spans associated with this locus shard. + * @return A list of the file spans to use when retrieving locus data. */ - public Map> getChunks() { - return chunks; + @Override + public Map getFileSpans() { + return fileSpans; } /** @@ -80,36 +80,42 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa * than just holding pointers to their locations. * @return True if this shard can buffer reads. False otherwise. */ + @Override public boolean buffersReads() { return false; } /** * Returns true if the read buffer is currently full. * @return True if this shard's buffer is full (and the shard can buffer reads). */ + @Override public boolean isBufferEmpty() { throw new UnsupportedOperationException("This shard does not buffer reads."); } /** * Returns true if the read buffer is currently full. * @return True if this shard's buffer is full (and the shard can buffer reads). */ + @Override public boolean isBufferFull() { throw new UnsupportedOperationException("This shard does not buffer reads."); } /** * Adds a read to the read buffer. * @param read Add a read to the internal shard buffer. */ + @Override public void addRead(SAMRecord read) { throw new UnsupportedOperationException("This shard does not buffer reads."); } /** * Gets the iterator over the elements cached in the shard. * @return */ + @Override public StingSAMIterator iterator() { throw new UnsupportedOperationException("This shard does not buffer reads."); } /** * Gets a filter testing for overlap of this read with the given shard. * @return A filter capable of filtering out reads outside a given shard. */ + @Override public SamRecordFilter getFilter() { return new ReadOverlapFilter(loci); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java index 20c44b994..64fdc8457 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java @@ -11,9 +11,9 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; import java.util.*; -import net.sf.samtools.Chunk; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMSequenceRecord; +import net.sf.samtools.BAMFileSpan; /* * Copyright (c) 2009 The Broad Institute @@ -126,8 +126,8 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy { */ public IndexDelimitedLocusShard next() { FilePointer nextFilePointer = filePointerIterator.next(); - Map> chunksBounding = nextFilePointer.chunks != null ? nextFilePointer.chunks : null; - return new IndexDelimitedLocusShard(nextFilePointer.locations,chunksBounding,Shard.ShardType.LOCUS_INTERVAL); + Map fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null; + return new IndexDelimitedLocusShard(nextFilePointer.locations,fileSpansBounding,Shard.ShardType.LOCUS_INTERVAL); } /** we don't support the remove command */ diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java index 311c8a94f..4dba5cdf2 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java @@ -172,7 +172,7 @@ public class IntervalSharder { for(SAMReaderID id: dataSource.getReaderIDs()) { PreloadedBAMFileIndex index = readerToIndexMap.get(id); for(FilePointer filePointer: filePointers) - filePointer.addChunks(id,index.getChunksOverlapping(filePointer.overlap.getBin(id))); + filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id))); index.close(); } @@ -372,7 +372,7 @@ public class IntervalSharder { * Represents a small section of a BAM file, and every associated interval. */ class FilePointer { - protected final Map> chunks = new HashMap>(); + protected final Map fileSpans = new HashMap(); protected final String referenceSequence; protected final BAMOverlap overlap; protected final List locations; @@ -393,8 +393,8 @@ class FilePointer { locations.add(location); } - public void addChunks(SAMReaderID id, List chunks) { - this.chunks.put(id,chunks); + public void addFileSpans(SAMReaderID id, BAMFileSpan fileSpan) { + this.fileSpans.put(id,fileSpan); } } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java index 1892da25a..f25bcf357 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java @@ -6,7 +6,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIteratorAdapter; import org.broadinstitute.sting.utils.StingException; -import org.broadinstitute.sting.utils.GenomeLoc; import net.sf.samtools.*; import net.sf.samtools.util.CloseableIterator; import net.sf.picard.sam.SamFileHeaderMerger; @@ -54,7 +53,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { /** * How far along is each reader? */ - private final Map readerPositions = new HashMap(); + private final Map readerPositions = new HashMap(); /** * Create a new block-aware SAM data source given the supplied read metadata. @@ -81,7 +80,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { } initializeReaderPositions(readers); - + SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true); mergedHeader = headerMerger.getMergedHeader(); hasReadGroupCollisions = headerMerger.hasReadGroupCollisions(); @@ -139,7 +138,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { * Retrieves the current position within the BAM file. * @return A mapping of reader to current position. */ - public Map getCurrentPosition() { + public Map getCurrentPosition() { return readerPositions; } @@ -183,7 +182,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { * @param read The read to add to the shard. */ private void addReadToBufferingShard(BAMFormatAwareShard shard,SAMReaderID id,SAMRecord read) { - Chunk endChunk = new Chunk(read.getCoordinates().getChunkEnd(),Long.MAX_VALUE); + BAMFileSpan endChunk = read.getFilePointer().getFilePointerFollowing(); shard.addRead(read); readerPositions.put(id,endChunk); } @@ -202,11 +201,15 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { throw new StingException("Unable to find id for reader associated with read " + read.getReadName()); } + /** + * Initialize the current reader positions + * @param readers + */ private void initializeReaderPositions(SAMReaders readers) { for(SAMReaderID id: getReaderIDs()) - readerPositions.put(id,readers.getReader(id).getCurrentPosition()); + readerPositions.put(id,readers.getReader(id).getStartOfDataSegment()); } - + public StingSAMIterator seek(Shard shard) { // todo: refresh monolithic sharding implementation if(shard instanceof MonolithicShard) @@ -236,9 +239,9 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { private StingSAMIterator getIterator(SAMReaders readers, BAMFormatAwareShard shard, boolean enableVerification) { Map> readerToIteratorMap = new HashMap>(); for(SAMReaderID id: getReaderIDs()) { - if(shard.getChunks().get(id) == null) + if(shard.getFileSpans().get(id) == null) continue; - CloseableIterator iterator = readers.getReader(id).iterator(shard.getChunks().get(id)); + CloseableIterator iterator = readers.getReader(id).iterator(shard.getFileSpans().get(id)); if(shard.getFilter() != null) iterator = new FilteringIterator(iterator,shard.getFilter()); readerToIteratorMap.put(readers.getReader(id),iterator); diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/ReferenceGraph.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/ReferenceGraph.java index 62036ea57..f7850e68d 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/ReferenceGraph.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/ReferenceGraph.java @@ -6,6 +6,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.genotype.Variation; import net.sf.picard.reference.ReferenceSequence; +import net.sf.picard.util.IntervalTree; import net.sf.samtools.util.StringUtil; import java.util.*; @@ -14,8 +15,6 @@ import java.io.IOException; import java.io.ObjectOutputStream; import java.io.ObjectInputStream; -import edu.mit.broad.picard.util.IntervalTree; - /** * Created by IntelliJ IDEA. * User: depristo diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java index 6f89a473f..8d095aa36 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java @@ -22,9 +22,9 @@ import java.io.File; import net.sf.samtools.SAMRecord; import net.sf.samtools.util.StringUtil; import net.sf.picard.reference.ReferenceSequence; -import edu.mit.broad.picard.util.Interval; -import edu.mit.broad.picard.util.OverlapDetector; -import edu.mit.broad.picard.directed.IntervalList; +import net.sf.picard.util.Interval; +import net.sf.picard.util.OverlapDetector; +import net.sf.picard.util.IntervalList; /** * Given intervals corresponding to targets or baits in a hybrid selection experiment, this walker gives the following interval-by-interval data: diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java index 3161007d4..0d9c7463a 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/GenotypeConcordance.java @@ -4,9 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; - - import java.io.*; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java index 5d35c04d7..2fe2977a4 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFApplyCuts.java @@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java index 2da54cd8f..1233b0b6b 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFCallRates.java @@ -4,13 +4,11 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; - - import java.io.*; import java.util.*; import net.sf.picard.PicardException; +import net.sf.picard.util.Interval; import net.sf.picard.io.IoUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java index cc0d72ce0..2878cc8e5 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFHomogenizer.java @@ -4,9 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; - - import java.io.*; import java.util.*; import java.util.zip.*; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java index dee796b0d..7ef3063b6 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFMerge.java @@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; @@ -14,6 +13,7 @@ import java.io.*; import java.util.*; import net.sf.picard.PicardException; +import net.sf.picard.util.Interval; import net.sf.picard.io.IoUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java index 4ed7448aa..993fa2ea3 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFOptimize.java @@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.Utils; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java index b15194bff..05acba408 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis.java @@ -4,13 +4,11 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; - - import java.io.*; import java.util.*; import net.sf.picard.PicardException; +import net.sf.picard.util.Interval; import net.sf.picard.io.IoUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java index d643eecdc..26d2877f2 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFSequenomAnalysis2.java @@ -4,14 +4,12 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; - - import java.io.*; import java.util.*; import java.lang.*; import net.sf.picard.PicardException; +import net.sf.picard.util.Interval; import net.sf.picard.io.IoUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; diff --git a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java index 80e8161e9..4f25da9f0 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java +++ b/java/src/org/broadinstitute/sting/playground/tools/vcf/VCFTool.java @@ -4,7 +4,6 @@ import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; -import edu.mit.broad.picard.util.Interval; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -14,6 +13,7 @@ import java.util.*; import java.util.zip.*; import net.sf.picard.PicardException; +import net.sf.picard.util.Interval; import net.sf.picard.io.IoUtil; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.ReferenceSequenceFile; diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index 6ffd63c7d..2a9e83e16 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils; -import edu.mit.broad.picard.directed.IntervalList; -import edu.mit.broad.picard.util.Interval; +import net.sf.picard.util.IntervalList; +import net.sf.picard.util.Interval; import net.sf.picard.reference.ReferenceSequenceFile; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMSequenceDictionary; diff --git a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index d25f6803c..0dd5a90f2 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -341,5 +341,5 @@ public class GATKSAMRecord extends SAMRecord { public String toString() { return mRecord.toString(); } - public Chunk getCoordinates() { return mRecord.getCoordinates(); } + public BAMFileSpan getFilePointer() { return mRecord.getFilePointer(); } } diff --git a/packages/PicardPrivate.xml b/packages/PicardPrivate.xml index 06f5235c7..20412c162 100644 --- a/packages/PicardPrivate.xml +++ b/packages/PicardPrivate.xml @@ -2,16 +2,12 @@ - - - - diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.jar b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar similarity index 64% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar index f8fc13d6d..840bb9824 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml similarity index 55% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml index acccf2e28..c358868fb 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-4.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.16.364-sharding.jar b/settings/repository/net.sf/picard-1.16.365-sharding.jar similarity index 96% rename from settings/repository/net.sf/picard-1.16.364-sharding.jar rename to settings/repository/net.sf/picard-1.16.365-sharding.jar index fc60bbb51..654a6bd76 100644 Binary files a/settings/repository/net.sf/picard-1.16.364-sharding.jar and b/settings/repository/net.sf/picard-1.16.365-sharding.jar differ diff --git a/settings/repository/net.sf/picard-1.16.364-sharding.xml b/settings/repository/net.sf/picard-1.16.365-sharding.xml similarity index 76% rename from settings/repository/net.sf/picard-1.16.364-sharding.xml rename to settings/repository/net.sf/picard-1.16.365-sharding.xml index b731a711d..f3f1d873c 100644 --- a/settings/repository/net.sf/picard-1.16.364-sharding.xml +++ b/settings/repository/net.sf/picard-1.16.365-sharding.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/sam-1.16.364-sharding.jar b/settings/repository/net.sf/sam-1.16.365-sharding.jar similarity index 79% rename from settings/repository/net.sf/sam-1.16.364-sharding.jar rename to settings/repository/net.sf/sam-1.16.365-sharding.jar index 7453d10ea..15571057f 100644 Binary files a/settings/repository/net.sf/sam-1.16.364-sharding.jar and b/settings/repository/net.sf/sam-1.16.365-sharding.jar differ diff --git a/settings/repository/net.sf/sam-1.16.364-sharding.xml b/settings/repository/net.sf/sam-1.16.365-sharding.xml similarity index 52% rename from settings/repository/net.sf/sam-1.16.364-sharding.xml rename to settings/repository/net.sf/sam-1.16.365-sharding.xml index 598c75488..f9aa3ca37 100644 --- a/settings/repository/net.sf/sam-1.16.364-sharding.xml +++ b/settings/repository/net.sf/sam-1.16.365-sharding.xml @@ -1,3 +1,3 @@ - +