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Revisions to take into account finalization of Picard patch: naming changes, better definition 

of public interfaces.  This won't be the last Picard patch, but it should be the last big one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-30 19:28:14 +00:00
parent b00d2bf2bc
commit 400684542c
15 changed files with 41 additions and 41 deletions
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2
java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java
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@ -74,7 +74,7 @@ public class BAMFileStat extends CommandLineProgram {
inspector.inspect(System.out,null,null); inspector.inspect(System.out,null,null);
} }
private class BAMFileIndexContentInspector extends PreloadedBAMFileIndex { private class BAMFileIndexContentInspector extends CachingBAMFileIndex {
public BAMFileIndexContentInspector(File bamFileIndex) { public BAMFileIndexContentInspector(File bamFileIndex) {
super(bamFileIndex); super(bamFileIndex);
} }

2
java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java
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@ -20,7 +20,7 @@ public interface BAMFormatAwareShard extends Shard {
* Get the list of chunks delimiting this shard. * Get the list of chunks delimiting this shard.
* @return a list of chunks that contain data for this shard. * @return a list of chunks that contain data for this shard.
*/ */
public Map<SAMReaderID, BAMFileSpan> getFileSpans(); public Map<SAMReaderID,SAMFileSpan> getFileSpans();
/** /**
* Returns true if this shard is meant to buffer reads, rather * Returns true if this shard is meant to buffer reads, rather

8
java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java
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@ -26,7 +26,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
/** /**
* The data backing the next chunks to deliver to the traversal engine. * The data backing the next chunks to deliver to the traversal engine.
*/ */
private final Map<SAMReaderID,BAMFileSpan> fileSpans; private final Map<SAMReaderID,SAMFileSpan> fileSpans;
/** /**
* The reads making up this shard. * The reads making up this shard.
@ -44,7 +44,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
*/ */
private final Shard.ShardType shardType; private final Shard.ShardType shardType;
public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,BAMFileSpan> fileSpans, SamRecordFilter filter, Shard.ShardType shardType) { public BlockDelimitedReadShard(Reads sourceInfo, Map<SAMReaderID,SAMFileSpan> fileSpans, SamRecordFilter filter, Shard.ShardType shardType) {
this.sourceInfo = sourceInfo; this.sourceInfo = sourceInfo;
this.fileSpans = fileSpans; this.fileSpans = fileSpans;
this.filter = filter; this.filter = filter;
@ -109,7 +109,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
* @return a list of chunks that contain data for this shard. * @return a list of chunks that contain data for this shard.
*/ */
@Override @Override
public Map<SAMReaderID,BAMFileSpan> getFileSpans() { public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
return Collections.unmodifiableMap(fileSpans); return Collections.unmodifiableMap(fileSpans);
} }
@ -128,7 +128,7 @@ public class BlockDelimitedReadShard extends ReadShard implements BAMFormatAware
@Override @Override
public String toString() { public String toString() {
StringBuilder sb = new StringBuilder(); StringBuilder sb = new StringBuilder();
for(Map.Entry<SAMReaderID,BAMFileSpan> entry: fileSpans.entrySet()) { for(Map.Entry<SAMReaderID,SAMFileSpan> entry: fileSpans.entrySet()) {
sb.append(entry.getKey()); sb.append(entry.getKey());
sb.append(": "); sb.append(": ");
sb.append(entry.getValue()); sb.append(entry.getValue());

12
java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
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@ -55,7 +55,7 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
/** /**
* Ending position of the last shard in the file. * Ending position of the last shard in the file.
*/ */
private Map<SAMReaderID,BAMFileSpan> position; private Map<SAMReaderID,SAMFileSpan> position;
/** /**
* Create a new read shard strategy, loading read shards from the given BAM file. * Create a new read shard strategy, loading read shards from the given BAM file.
@ -103,18 +103,18 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
} }
public void advance() { public void advance() {
Map<SAMReaderID,BAMFileSpan> shardPosition = new HashMap<SAMReaderID,BAMFileSpan>(); Map<SAMReaderID,SAMFileSpan> shardPosition = new HashMap<SAMReaderID,SAMFileSpan>();
nextShard = null; nextShard = null;
SamRecordFilter filter = null; SamRecordFilter filter = null;
if(locations != null) { if(locations != null) {
Map<SAMReaderID,BAMFileSpan> selectedReaders = new HashMap<SAMReaderID,BAMFileSpan>(); Map<SAMReaderID,SAMFileSpan> selectedReaders = new HashMap<SAMReaderID,SAMFileSpan>();
while(selectedReaders.size() == 0 && currentFilePointer != null) { while(selectedReaders.size() == 0 && currentFilePointer != null) {
shardPosition = currentFilePointer.fileSpans; shardPosition = currentFilePointer.fileSpans;
for(SAMReaderID id: shardPosition.keySet()) { for(SAMReaderID id: shardPosition.keySet()) {
BAMFileSpan fileSpans = shardPosition.get(id).removeBefore(position.get(id)); SAMFileSpan fileSpan = shardPosition.get(id).removeContentsBefore(position.get(id));
if(!fileSpans.isEmpty()) if(!fileSpan.isEmpty())
selectedReaders.put(id,fileSpans); selectedReaders.put(id,fileSpan);
} }
if(selectedReaders.size() > 0) { if(selectedReaders.size() > 0) {

8
java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java
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@ -5,7 +5,7 @@ import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import net.sf.samtools.BAMFileSpan; import net.sf.samtools.SAMFileSpan;
import net.sf.picard.filter.SamRecordFilter; import net.sf.picard.filter.SamRecordFilter;
import java.util.List; import java.util.List;
@ -44,7 +44,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
/** /**
* A list of the chunks associated with this shard. * A list of the chunks associated with this shard.
*/ */
private final Map<SAMReaderID, BAMFileSpan> fileSpans; private final Map<SAMReaderID,SAMFileSpan> fileSpans;
/** /**
* An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types. * An IndexDelimitedLocusShard can be used either for LOCUS or LOCUS_INTERVAL shard types.
@ -58,7 +58,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
* @param fileSpans File spans 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. * @param shardType Type of the shard; must be either LOCUS or LOCUS_INTERVAL.
*/ */
IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,BAMFileSpan> fileSpans, ShardType shardType) { IndexDelimitedLocusShard(List<GenomeLoc> intervals, Map<SAMReaderID,SAMFileSpan> fileSpans, ShardType shardType) {
super(intervals); super(intervals);
this.fileSpans = fileSpans; this.fileSpans = fileSpans;
if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL) if(shardType != ShardType.LOCUS && shardType != ShardType.LOCUS_INTERVAL)
@ -71,7 +71,7 @@ public class IndexDelimitedLocusShard extends LocusShard implements BAMFormatAwa
* @return A list of the file spans to use when retrieving locus data. * @return A list of the file spans to use when retrieving locus data.
*/ */
@Override @Override
public Map<SAMReaderID,BAMFileSpan> getFileSpans() { public Map<SAMReaderID,SAMFileSpan> getFileSpans() {
return fileSpans; return fileSpans;
} }

4
java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java
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@ -13,7 +13,7 @@ import java.util.*;
import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.BAMFileSpan; import net.sf.samtools.SAMFileSpan;
/* /*
* Copyright (c) 2009 The Broad Institute * Copyright (c) 2009 The Broad Institute
@ -126,7 +126,7 @@ public class IndexDelimitedLocusShardStrategy implements ShardStrategy {
*/ */
public IndexDelimitedLocusShard next() { public IndexDelimitedLocusShard next() {
FilePointer nextFilePointer = filePointerIterator.next(); FilePointer nextFilePointer = filePointerIterator.next();
Map<SAMReaderID, BAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null; Map<SAMReaderID,SAMFileSpan> fileSpansBounding = nextFilePointer.fileSpans != null ? nextFilePointer.fileSpans : null;
return new IndexDelimitedLocusShard(nextFilePointer.locations,fileSpansBounding,Shard.ShardType.LOCUS_INTERVAL); return new IndexDelimitedLocusShard(nextFilePointer.locations,fileSpansBounding,Shard.ShardType.LOCUS_INTERVAL);
} }

24
java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
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@ -75,11 +75,11 @@ public class IntervalSharder {
FilePointer lastFilePointer = null; FilePointer lastFilePointer = null;
BAMOverlap lastBAMOverlap = null; BAMOverlap lastBAMOverlap = null;
Map<SAMReaderID,PreloadedBAMFileIndex> readerToIndexMap = new HashMap<SAMReaderID,PreloadedBAMFileIndex>(); Map<SAMReaderID,CachingBAMFileIndex> readerToIndexMap = new HashMap<SAMReaderID,CachingBAMFileIndex>();
BinMergingIterator binMerger = new BinMergingIterator(); BinMergingIterator binMerger = new BinMergingIterator();
for(SAMReaderID id: dataSource.getReaderIDs()) { for(SAMReaderID id: dataSource.getReaderIDs()) {
final SAMSequenceRecord referenceSequence = dataSource.getHeader(id).getSequence(contig); final SAMSequenceRecord referenceSequence = dataSource.getHeader(id).getSequence(contig);
final PreloadedBAMFileIndex index = dataSource.getIndex(id); final CachingBAMFileIndex index = dataSource.getIndex(id);
binMerger.addReader(id, binMerger.addReader(id,
index, index,
referenceSequence.getSequenceIndex(), referenceSequence.getSequenceIndex(),
@ -170,7 +170,7 @@ public class IntervalSharder {
// Lookup the locations for every file pointer in the index. // Lookup the locations for every file pointer in the index.
for(SAMReaderID id: dataSource.getReaderIDs()) { for(SAMReaderID id: dataSource.getReaderIDs()) {
PreloadedBAMFileIndex index = readerToIndexMap.get(id); CachingBAMFileIndex index = readerToIndexMap.get(id);
for(FilePointer filePointer: filePointers) for(FilePointer filePointer: filePointers)
filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id))); filePointer.addFileSpans(id,index.getChunksOverlapping(filePointer.overlap.getBin(id)));
index.close(); index.close();
@ -183,7 +183,7 @@ public class IntervalSharder {
private PriorityQueue<BinQueueState> binQueue = new PriorityQueue<BinQueueState>(); private PriorityQueue<BinQueueState> binQueue = new PriorityQueue<BinQueueState>();
private Queue<BAMOverlap> pendingOverlaps = new LinkedList<BAMOverlap>(); private Queue<BAMOverlap> pendingOverlaps = new LinkedList<BAMOverlap>();
public void addReader(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, Iterator<Bin> bins) { public void addReader(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, Iterator<Bin> bins) {
binQueue.add(new BinQueueState(id,index,referenceSequence,new LowestLevelBinFilteringIterator(index,bins))); binQueue.add(new BinQueueState(id,index,referenceSequence,new LowestLevelBinFilteringIterator(index,bins)));
} }
@ -276,11 +276,11 @@ public class IntervalSharder {
private class ReaderBin { private class ReaderBin {
public final SAMReaderID id; public final SAMReaderID id;
public final PreloadedBAMFileIndex index; public final CachingBAMFileIndex index;
public final int referenceSequence; public final int referenceSequence;
public final Bin bin; public final Bin bin;
public ReaderBin(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Bin bin) { public ReaderBin(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, final Bin bin) {
this.id = id; this.id = id;
this.index = index; this.index = index;
this.referenceSequence = referenceSequence; this.referenceSequence = referenceSequence;
@ -298,11 +298,11 @@ public class IntervalSharder {
private class BinQueueState implements Comparable<BinQueueState> { private class BinQueueState implements Comparable<BinQueueState> {
public final SAMReaderID id; public final SAMReaderID id;
public final PreloadedBAMFileIndex index; public final CachingBAMFileIndex index;
public final int referenceSequence; public final int referenceSequence;
public final PeekableIterator<Bin> bins; public final PeekableIterator<Bin> bins;
public BinQueueState(final SAMReaderID id, final PreloadedBAMFileIndex index, final int referenceSequence, final Iterator<Bin> bins) { public BinQueueState(final SAMReaderID id, final CachingBAMFileIndex index, final int referenceSequence, final Iterator<Bin> bins) {
this.id = id; this.id = id;
this.index = index; this.index = index;
this.referenceSequence = referenceSequence; this.referenceSequence = referenceSequence;
@ -334,12 +334,12 @@ public class IntervalSharder {
* Filters out bins not at the lowest level in the tree. * Filters out bins not at the lowest level in the tree.
*/ */
private static class LowestLevelBinFilteringIterator implements Iterator<Bin> { private static class LowestLevelBinFilteringIterator implements Iterator<Bin> {
private PreloadedBAMFileIndex index; private CachingBAMFileIndex index;
private Iterator<Bin> wrappedIterator; private Iterator<Bin> wrappedIterator;
private Bin nextBin; private Bin nextBin;
public LowestLevelBinFilteringIterator(final PreloadedBAMFileIndex index, Iterator<Bin> iterator) { public LowestLevelBinFilteringIterator(final CachingBAMFileIndex index, Iterator<Bin> iterator) {
this.index = index; this.index = index;
this.wrappedIterator = iterator; this.wrappedIterator = iterator;
advance(); advance();
@ -372,7 +372,7 @@ public class IntervalSharder {
* Represents a small section of a BAM file, and every associated interval. * Represents a small section of a BAM file, and every associated interval.
*/ */
class FilePointer { class FilePointer {
protected final Map<SAMReaderID,BAMFileSpan> fileSpans = new HashMap<SAMReaderID,BAMFileSpan>(); protected final Map<SAMReaderID,SAMFileSpan> fileSpans = new HashMap<SAMReaderID,SAMFileSpan>();
protected final String referenceSequence; protected final String referenceSequence;
protected final BAMOverlap overlap; protected final BAMOverlap overlap;
protected final List<GenomeLoc> locations; protected final List<GenomeLoc> locations;
@ -393,7 +393,7 @@ class FilePointer {
locations.add(location); locations.add(location);
} }
public void addFileSpans(SAMReaderID id, BAMFileSpan fileSpan) { public void addFileSpans(SAMReaderID id, SAMFileSpan fileSpan) {
this.fileSpans.put(id,fileSpan); this.fileSpans.put(id,fileSpan);
} }
} }

14
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java
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@ -53,7 +53,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
/** /**
* How far along is each reader? * How far along is each reader?
*/ */
private final Map<SAMReaderID,BAMFileSpan> readerPositions = new HashMap<SAMReaderID,BAMFileSpan>(); private final Map<SAMReaderID,SAMFileSpan> readerPositions = new HashMap<SAMReaderID,SAMFileSpan>();
/** /**
* Create a new block-aware SAM data source given the supplied read metadata. * Create a new block-aware SAM data source given the supplied read metadata.
@ -129,16 +129,16 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
* @param id Id of the reader. * @param id Id of the reader.
* @return The index. Will preload the index if necessary. * @return The index. Will preload the index if necessary.
*/ */
public PreloadedBAMFileIndex getIndex(final SAMReaderID id) { public CachingBAMFileIndex getIndex(final SAMReaderID id) {
SAMReaders readers = resourcePool.getReadersWithoutLocking(); SAMReaders readers = resourcePool.getReadersWithoutLocking();
return readers.getReader(id).getIndex(PreloadedBAMFileIndex.class); return readers.getReader(id).getIndex(CachingBAMFileIndex.class);
} }
/** /**
* Retrieves the current position within the BAM file. * Retrieves the current position within the BAM file.
* @return A mapping of reader to current position. * @return A mapping of reader to current position.
*/ */
public Map<SAMReaderID,BAMFileSpan> getCurrentPosition() { public Map<SAMReaderID,SAMFileSpan> getCurrentPosition() {
return readerPositions; return readerPositions;
} }
@ -182,7 +182,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
* @param read The read to add to the shard. * @param read The read to add to the shard.
*/ */
private void addReadToBufferingShard(BAMFormatAwareShard shard,SAMReaderID id,SAMRecord read) { private void addReadToBufferingShard(BAMFormatAwareShard shard,SAMReaderID id,SAMRecord read) {
BAMFileSpan endChunk = read.getFilePointer().getFilePointerFollowing(); SAMFileSpan endChunk = read.getFilePointer().getContentsFollowing();
shard.addRead(read); shard.addRead(read);
readerPositions.put(id,endChunk); readerPositions.put(id,endChunk);
} }
@ -207,7 +207,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
*/ */
private void initializeReaderPositions(SAMReaders readers) { private void initializeReaderPositions(SAMReaders readers) {
for(SAMReaderID id: getReaderIDs()) for(SAMReaderID id: getReaderIDs())
readerPositions.put(id,readers.getReader(id).getStartOfDataSegment()); readerPositions.put(id,readers.getReader(id).getFilePointerSpanningReads());
} }
public StingSAMIterator seek(Shard shard) { public StingSAMIterator seek(Shard shard) {
@ -386,7 +386,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource {
*/ */
public SAMReaders(Reads sourceInfo) { public SAMReaders(Reads sourceInfo) {
for(File readsFile: sourceInfo.getReadsFiles()) { for(File readsFile: sourceInfo.getReadsFiles()) {
SAMFileReader reader = new SAMFileReader(readsFile,true); SAMFileReader reader = new SAMFileReader(readsFile,CachingBAMFileIndex.class,true);
reader.setValidationStringency(sourceInfo.getValidationStringency()); reader.setValidationStringency(sourceInfo.getValidationStringency());
// If no read group is present, hallucinate one. // If no read group is present, hallucinate one.

2
java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -341,5 +341,5 @@ public class GATKSAMRecord extends SAMRecord {
public String toString() { return mRecord.toString(); } public String toString() { return mRecord.toString(); }
public BAMFileSpan getFilePointer() { return mRecord.getFilePointer(); } public SAMFileSpan getFilePointer() { return mRecord.getFilePointer(); }
} }

BIN
settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.jar → settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.jar
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2
settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-5.xml → settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-6.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-5" status="integration" publication="20100326102100" /> <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-6" status="integration" publication="20100330130700" />
</ivy-module> </ivy-module>

BIN
settings/repository/net.sf/picard-1.16.365-sharding.jar → settings/repository/net.sf/picard-1.16.366-sharding.jar
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2
settings/repository/net.sf/picard-1.16.365-sharding.xml → settings/repository/net.sf/picard-1.16.366-sharding.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.16.365-sharding" status="release" /> <info organisation="net.sf" module="picard" revision="1.16.366-sharding" status="release" />
</ivy-module> </ivy-module>

BIN
settings/repository/net.sf/sam-1.16.365-sharding.jar → settings/repository/net.sf/sam-1.16.366-sharding.jar
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2
settings/repository/net.sf/sam-1.16.365-sharding.xml → settings/repository/net.sf/sam-1.16.366-sharding.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.16.365-sharding" status="release" /> <info organisation="net.sf" module="sam" revision="1.16.366-sharding" status="release" />
</ivy-module> </ivy-module>