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 5e83ea330..c47df9e95 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BAMFormatAwareShard.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader2; +import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMRecord; import net.sf.picard.filter.SamRecordFilter; 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 fb0f3a248..761a46de8 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/BlockDelimitedReadShard.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.datasources.shards; import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader2; +import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMRecord; import net.sf.picard.filter.SamRecordFilter; 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 3ed9230a7..35bd1b94c 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShard.java @@ -5,7 +5,7 @@ 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.SAMFileReader2; +import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMRecord; import net.sf.picard.filter.SamRecordFilter; 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 47e95e499..d428064d3 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IndexDelimitedLocusShardStrategy.java @@ -12,7 +12,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; import java.util.*; import net.sf.samtools.Chunk; -import net.sf.samtools.SAMFileReader2; +import net.sf.samtools.SAMFileReader; import net.sf.samtools.SAMFileHeader; import net.sf.samtools.SAMSequenceRecord; 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 f1e5c48dd..1892da25a 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/BlockDrivenSAMDataSource.java @@ -132,7 +132,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { */ public PreloadedBAMFileIndex getIndex(final SAMReaderID id) { SAMReaders readers = resourcePool.getReadersWithoutLocking(); - return ((SAMFileReader2)readers.getReader(id)).getIndex(PreloadedBAMFileIndex.class); + return readers.getReader(id).getIndex(PreloadedBAMFileIndex.class); } /** @@ -203,10 +203,8 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { } private void initializeReaderPositions(SAMReaders readers) { - for(SAMReaderID id: getReaderIDs()) { - SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id); - readerPositions.put(id,reader2.getCurrentPosition()); - } + for(SAMReaderID id: getReaderIDs()) + readerPositions.put(id,readers.getReader(id).getCurrentPosition()); } public StingSAMIterator seek(Shard shard) { @@ -238,13 +236,12 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { private StingSAMIterator getIterator(SAMReaders readers, BAMFormatAwareShard shard, boolean enableVerification) { Map> readerToIteratorMap = new HashMap>(); for(SAMReaderID id: getReaderIDs()) { - SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id); if(shard.getChunks().get(id) == null) continue; - CloseableIterator iterator = reader2.iterator(shard.getChunks().get(id)); + CloseableIterator iterator = readers.getReader(id).iterator(shard.getChunks().get(id)); if(shard.getFilter() != null) iterator = new FilteringIterator(iterator,shard.getFilter()); - readerToIteratorMap.put(reader2,iterator); + readerToIteratorMap.put(readers.getReader(id),iterator); } SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true); @@ -268,10 +265,8 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { SAMReaders readers = resourcePool.getAvailableReaders(); Map> readerToIteratorMap = new HashMap>(); - for(SAMReaderID id: getReaderIDs()) { - SAMFileReader2 reader2 = (SAMFileReader2)readers.getReader(id); - readerToIteratorMap.put(reader2,reader2.iterator()); - } + for(SAMReaderID id: getReaderIDs()) + readerToIteratorMap.put(readers.getReader(id),readers.getReader(id).iterator()); // Set up merging and filtering to dynamically merge together multiple BAMs and filter out records not in the shard set. SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true); @@ -388,7 +383,7 @@ public class BlockDrivenSAMDataSource extends SAMDataSource { */ public SAMReaders(Reads sourceInfo) { for(File readsFile: sourceInfo.getReadsFiles()) { - SAMFileReader2 reader = new SAMFileReader2(readsFile,true); + SAMFileReader reader = new SAMFileReader(readsFile,true); reader.setValidationStringency(sourceInfo.getValidationStringency()); // If no read group is present, hallucinate one. diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.jar b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar similarity index 86% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar index f82382429..568416b9b 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.xml b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml similarity index 66% rename from settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml index 1b4c6f437..7beba5fb1 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-1.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-2.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.16.360-sharding.jar b/settings/repository/net.sf/picard-1.16.362-sharding.jar similarity index 95% rename from settings/repository/net.sf/picard-1.16.360-sharding.jar rename to settings/repository/net.sf/picard-1.16.362-sharding.jar index 6a500f4ad..8f28163ba 100644 Binary files a/settings/repository/net.sf/picard-1.16.360-sharding.jar and b/settings/repository/net.sf/picard-1.16.362-sharding.jar differ diff --git a/settings/repository/net.sf/picard-1.16.360-sharding.xml b/settings/repository/net.sf/picard-1.16.362-sharding.xml similarity index 76% rename from settings/repository/net.sf/picard-1.16.360-sharding.xml rename to settings/repository/net.sf/picard-1.16.362-sharding.xml index fa201033a..8605edce7 100644 --- a/settings/repository/net.sf/picard-1.16.360-sharding.xml +++ b/settings/repository/net.sf/picard-1.16.362-sharding.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/sam-1.16.360-sharding.jar b/settings/repository/net.sf/sam-1.16.362-sharding.jar similarity index 84% rename from settings/repository/net.sf/sam-1.16.360-sharding.jar rename to settings/repository/net.sf/sam-1.16.362-sharding.jar index 837e020e0..ef72fa9cf 100644 Binary files a/settings/repository/net.sf/sam-1.16.360-sharding.jar and b/settings/repository/net.sf/sam-1.16.362-sharding.jar differ diff --git a/settings/repository/net.sf/sam-1.16.360-sharding.xml b/settings/repository/net.sf/sam-1.16.362-sharding.xml similarity index 52% rename from settings/repository/net.sf/sam-1.16.360-sharding.xml rename to settings/repository/net.sf/sam-1.16.362-sharding.xml index 1a7d7736b..7692bcd7d 100644 --- a/settings/repository/net.sf/sam-1.16.360-sharding.xml +++ b/settings/repository/net.sf/sam-1.16.362-sharding.xml @@ -1,3 +1,3 @@ - +