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Oops! Introduced a performance bug in read interval sharding, when the new sharding system is available. Track more state to avoid this problem in the future. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2987 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-11 23:19:42 +00:00
parent 740238b4fa
commit 5e8654fcdc
2 changed files with 24 additions and 7 deletions
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29
java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShardStrategy.java
View File

@ -35,7 +35,17 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
private final List<FilePointer> filePointers = new ArrayList<FilePointer>();
/**
* Position of the last shard in the file.
* Iterator over the list of file pointers.
*/
private final Iterator<FilePointer> filePointerIterator;
/**
* The file pointer currently being processed.
*/
private FilePointer currentFilePointer;
/**
* Ending position of the last shard in the file.
*/
private Map<SAMReaderID,Chunk> position;
@ -51,6 +61,11 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
this.position = this.dataSource.getCurrentPosition();
if(locations != null)
filePointers.addAll(IntervalSharder.shardIntervals(this.dataSource,locations.toList(),this.dataSource.getNumIndexLevels()-1));
filePointerIterator = filePointers.iterator();
if(filePointerIterator.hasNext())
currentFilePointer = filePointerIterator.next();
advance();
}
@ -81,10 +96,10 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
SamRecordFilter filter = null;
if(!filePointers.isEmpty()) {
for(FilePointer filePointer: filePointers) {
shardPosition = dataSource.getFilePointersBounding(filePointer.bin);
Map<SAMReaderID,List<Chunk>> selectedReaders = new HashMap<SAMReaderID,List<Chunk>>();
while(selectedReaders.size() == 0 && currentFilePointer != null) {
shardPosition = dataSource.getFilePointersBounding(currentFilePointer.bin);
Map<SAMReaderID,List<Chunk>> selectedReaders = new HashMap<SAMReaderID,List<Chunk>>();
for(SAMReaderID id: shardPosition.keySet()) {
List<Chunk> chunks = shardPosition.get(id);
List<Chunk> selectedChunks = new ArrayList<Chunk>();
@ -98,17 +113,19 @@ public class BlockDelimitedReadShardStrategy extends ReadShardStrategy {
if(selectedChunks.size() > 0)
selectedReaders.put(id,selectedChunks);
}
if(selectedReaders.size() > 0) {
filter = new ReadOverlapFilter(filePointer.locations);
if(selectedReaders.size() > 0) {
BAMFormatAwareShard shard = new BlockDelimitedReadShard(dataSource.getReadsInfo(),selectedReaders,filter,Shard.ShardType.READ);
dataSource.fillShard(shard);
if(!shard.isBufferEmpty()) {
filter = new ReadOverlapFilter(currentFilePointer.locations);
nextShard = shard;
break;
}
}
currentFilePointer = filePointerIterator.hasNext() ? filePointerIterator.next() : null;
}
}
else {

2
java/src/org/broadinstitute/sting/gatk/datasources/shards/ReadDelimitedReadShardStrategy.java
View File

@ -11,7 +11,7 @@ import java.util.Iterator;
*/
public class ReadDelimitedReadShardStrategy extends ReadShardStrategy {
// our read bucket size, default
protected long readCount = 100000L;
protected long readCount = 1000L;
// our hasnext flag
boolean hasNext = true;