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A bit of reorganization to help with more flexible output streams. Pushed construction of data 

sources and post-construction validation back into the GATKEngine, leaving the MicroScheduler
to just microschedule.  


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1336 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-29 23:00:15 +00:00
parent bca894ebce
commit 5429b4d4a8
15 changed files with 180 additions and 217 deletions
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226
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -26,11 +26,9 @@
package org.broadinstitute.sting.gatk;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.picard.reference.ReferenceSequenceFileFactory;
import net.sf.picard.sam.SamFileHeaderMerger;
import net.sf.picard.filter.SamRecordFilter;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.*;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
@ -40,7 +38,6 @@ import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.executive.MicroScheduler;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.utils.*;
@ -58,9 +55,20 @@ public class GenomeAnalysisEngine {
// TODO: public static without final tends to indicate we're thinking about this the wrong way
public static GenomeAnalysisEngine instance;
// our traversal engine
private TraversalEngine engine = null;
private SAMDataSource dataSource = null;
/**
* Accessor for sharded read data.
*/
private SAMDataSource readsDataSource = null;
/**
* Accessor for sharded reference data.
*/
private IndexedFastaSequenceFile referenceDataSource = null;
/**
* Accessor for sharded reference-ordered data.
*/
private List<ReferenceOrderedDataSource> rodDataSources;
// our argument collection
private GATKArgumentCollection argCollection;
@ -105,55 +113,24 @@ public class GenomeAnalysisEngine {
// save our argument parameter
this.argCollection = args;
// our reference ordered data collection
List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
//
// please don't use these in the future, use the new syntax <- if we're not using these please remove them
//
if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile);
if (argCollection.HAPMAPFile != null)
bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
if (argCollection.HAPMAPChipFile != null)
bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
// TODO: The ROD iterator currently does not understand multiple intervals file. Fix this by cleaning the ROD system.
if (argCollection.intervals != null && argCollection.intervals.size() == 1) {
bindConvenienceRods("interval", "Intervals", argCollection.intervals.get(0).replaceAll(",", ""));
}
// parse out the rod bindings
ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);
// Validate the walker inputs against the walker.
validateInputsAgainstWalker(my_walker, argCollection, rods);
// Prepare the data for traversal.
initializeDataSources( my_walker, argCollection );
// our microscheduler, which is in charge of running everything
MicroScheduler microScheduler = createMicroscheduler(my_walker, rods);
MicroScheduler microScheduler = createMicroscheduler(my_walker);
// create the output streams
initializeOutputStreams(my_walker);
// Prepare the sort ordering w.r.t. the sequence dictionary
if (argCollection.referenceFile != null) {
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
GenomeLocParser.setupRefContigOrdering(refFile);
}
logger.info("Strictness is " + argCollection.strictnessLevel);
// perform validation steps that are common to all the engines
engine.setMaximumIterations(argCollection.maximumEngineIterations);
engine.initialize();
GenomeLocSortedSet locs = null;
if (argCollection.intervals != null) {
locs = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
}
ShardStrategy shardStrategy = this.getShardStrategy(my_walker, microScheduler.getReference(), locs, argCollection.maximumEngineIterations);
ShardStrategy shardStrategy = getShardStrategy(my_walker, microScheduler.getReference(), locs, argCollection.maximumEngineIterations);
// execute the microscheduler, storing the results
return microScheduler.execute(my_walker, shardStrategy);
return microScheduler.execute(my_walker, shardStrategy, argCollection.maximumEngineIterations);
}
/**
@ -182,28 +159,49 @@ public class GenomeAnalysisEngine {
return walkerManager.createWalkerByName(walkerName);
}
private void initializeDataSources( Walker my_walker, GATKArgumentCollection argCollection ) {
validateSuppliedReadsAgainstWalker( my_walker, argCollection );
logger.info("Strictness is " + argCollection.strictnessLevel);
readsDataSource = createReadsDataSource(extractSourceInfo(my_walker,argCollection));
validateSuppliedReferenceAgainstWalker( my_walker, argCollection );
referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
validateReadsAndReferenceAreCompatible(readsDataSource, referenceDataSource);
// our reference ordered data collection
List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods = new ArrayList<ReferenceOrderedData<? extends ReferenceOrderedDatum>>();
//
// please don't use these in the future, use the new syntax <- if we're not using these please remove them
//
if (argCollection.DBSNPFile != null) bindConvenienceRods("dbSNP", "dbsnp", argCollection.DBSNPFile);
if (argCollection.HAPMAPFile != null)
bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
if (argCollection.HAPMAPChipFile != null)
bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
// TODO: The ROD iterator currently does not understand multiple intervals file. Fix this by cleaning the ROD system.
if (argCollection.intervals != null && argCollection.intervals.size() == 1) {
bindConvenienceRods("interval", "Intervals", argCollection.intervals.get(0).replaceAll(",", ""));
}
// parse out the rod bindings
ReferenceOrderedData.parseBindings(logger, argCollection.RODBindings, rods);
validateSuppliedReferenceOrderedDataAgainstWalker( my_walker, rods );
rodDataSources = getReferenceOrderedDataSources(rods);
}
/**
* setup a microscheduler
*
* @param my_walker our walker of type LocusWalker
* @param rods the reference order data
*
* @return a new microscheduler
*/
private MicroScheduler createMicroscheduler(Walker my_walker, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
private MicroScheduler createMicroscheduler(Walker my_walker) {
// the mircoscheduler to return
MicroScheduler microScheduler = null;
SAMDataSource readsDataSource = createReadsDataSource(extractSourceInfo(my_walker,argCollection));
IndexedFastaSequenceFile referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
List<ReferenceOrderedDataSource> rodDataSources = getReferenceOrderedDataSources(rods);
GenomeLocSortedSet locs = null;
if (argCollection.intervals != null) {
locs = GenomeLocSortedSet.createSetFromList(parseIntervalRegion(argCollection.intervals));
}
// we need to verify different parameter based on the walker type
if (my_walker instanceof LocusWalker || my_walker instanceof LocusWindowWalker) {
// create the MicroScheduler
@ -216,9 +214,6 @@ public class GenomeAnalysisEngine {
Utils.scareUser(String.format("Unable to create the appropriate TraversalEngine for analysis type " + argCollection.analysisName));
}
dataSource = microScheduler.getSAMDataSource();
engine = microScheduler.getTraversalEngine();
return microScheduler;
}
@ -351,23 +346,43 @@ public class GenomeAnalysisEngine {
filters );
}
private void validateInputsAgainstWalker(Walker walker,
GATKArgumentCollection arguments,
List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods) {
String walkerName = WalkerManager.getWalkerName(walker.getClass());
/**
* Verifies that the supplied set of reads files mesh with what the walker says it requires.
* @param walker Walker to test.
* @param arguments Supplied reads files.
*/
private void validateSuppliedReadsAgainstWalker( Walker walker, GATKArgumentCollection arguments ) {
// Check what the walker says is required against what was provided on the command line.
if (WalkerManager.isRequired(walker, DataSource.READS) && (arguments.samFiles == null || arguments.samFiles.size() == 0))
throw new ArgumentException(String.format("Walker %s requires reads but none were provided. If this is incorrect, alter the walker's @Requires annotation.", walkerName));
if (WalkerManager.isRequired(walker, DataSource.REFERENCE) && arguments.referenceFile == null)
throw new ArgumentException(String.format("Walker %s requires a reference but none was provided. If this is incorrect, alter the walker's @Requires annotation.", walkerName));
throw new ArgumentException("Walker requires reads but none were provided. If this is incorrect, alter the walker's @Requires annotation.");
// Check what the walker says is allowed against what was provided on the command line.
if ((arguments.samFiles != null && arguments.samFiles.size() > 0) && !WalkerManager.isAllowed(walker, DataSource.READS))
throw new ArgumentException(String.format("Walker %s does not allow reads but reads were provided. If this is incorrect, alter the walker's @Allows annotation", walkerName));
if (arguments.referenceFile != null && !WalkerManager.isAllowed(walker, DataSource.REFERENCE))
throw new ArgumentException(String.format("Walker %s does not allow a reference but one was provided. If this is incorrect, alter the walker's @Allows annotation", walkerName));
throw new ArgumentException("Walker does not allow reads but reads were provided. If this is incorrect, alter the walker's @Allows annotation");
}
/**
* Verifies that the supplied reference file mesh with what the walker says it requires.
* @param walker Walker to test.
* @param arguments Supplied reads files.
*/
private void validateSuppliedReferenceAgainstWalker( Walker walker, GATKArgumentCollection arguments ) {
// Check what the walker says is required against what was provided on the command line.
if (WalkerManager.isRequired(walker, DataSource.REFERENCE) && arguments.referenceFile == null)
throw new ArgumentException("Walker requires a reference but none was provided. If this is incorrect, alter the walker's @Requires annotation.");
// Check what the walker says is allowed against what was provided on the command line.
if (arguments.referenceFile != null && !WalkerManager.isAllowed(walker, DataSource.REFERENCE))
throw new ArgumentException("Walker does not allow a reference but one was provided. If this is incorrect, alter the walker's @Allows annotation");
}
/**
* Verifies that all required reference-ordered data has been supplied, and any reference-ordered data that was not
* 'allowed' is still present.
* @param walker Walker to test.
* @param rods Reference-ordered data to load.
*/
private void validateSuppliedReferenceOrderedDataAgainstWalker( Walker walker, List<ReferenceOrderedData<? extends ReferenceOrderedDatum>> rods ) {
// Check to make sure that all required metadata is present.
List<RMD> allRequired = WalkerManager.getRequiredMetaData(walker);
for (RMD required : allRequired) {
@ -383,10 +398,73 @@ public class GenomeAnalysisEngine {
// Check to see that no forbidden rods are present.
for (ReferenceOrderedData<? extends ReferenceOrderedDatum> rod : rods) {
if (!WalkerManager.isAllowed(walker, rod))
throw new ArgumentException(String.format("Walker does not allow access to metadata: %s. If this is correct, change the @Allows metadata", rod.getName()));
throw new ArgumentException(String.format("Walker does not allow access to metadata: %s. If this is incorrect, change the @Allows metadata", rod.getName()));
}
}
/**
* Now that all files are open, validate the sequence dictionaries of the reads vs. the reference.
* @param reads Reads data source.
* @param reference Reference data source.
*/
private void validateReadsAndReferenceAreCompatible( SAMDataSource reads, ReferenceSequenceFile reference ) {
if( reads == null || reference == null )
return;
// Compile a set of sequence names that exist in the BAM files.
SAMSequenceDictionary readsDictionary = reads.getHeader().getSequenceDictionary();
Set<String> readsSequenceNames = new TreeSet<String>();
for( SAMSequenceRecord dictionaryEntry: readsDictionary.getSequences() )
readsSequenceNames.add(dictionaryEntry.getSequenceName());
// Compile a set of sequence names that exist in the reference file.
SAMSequenceDictionary referenceDictionary = reference.getSequenceDictionary();
Set<String> referenceSequenceNames = new TreeSet<String>();
for( SAMSequenceRecord dictionaryEntry: referenceDictionary.getSequences() )
referenceSequenceNames.add(dictionaryEntry.getSequenceName());
if( readsSequenceNames.size() == 0 ) {
logger.info("Reads file is unmapped. Skipping validation against reference.");
return;
}
// If there's no overlap between reads and reference, data will be bogus. Throw an exception.
Set<String> intersectingSequenceNames = new HashSet<String>(readsSequenceNames);
intersectingSequenceNames.retainAll(referenceSequenceNames);
if( intersectingSequenceNames.size() == 0 ) {
StringBuilder error = new StringBuilder();
error.append("No overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference. Perhaps you're using the wrong reference?\n");
error.append(System.getProperty("line.separator"));
error.append(String.format("Reads contigs: %s%n", prettyPrintSequenceRecords(readsDictionary)));
error.append(String.format("Reference contigs: %s%n", prettyPrintSequenceRecords(referenceDictionary)));
logger.error(error.toString());
Utils.scareUser("No overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference.");
}
// If the two datasets are not equal and neither is a strict subset of the other, warn the user.
if( !readsSequenceNames.equals(referenceSequenceNames) &&
!readsSequenceNames.containsAll(referenceSequenceNames) &&
!referenceSequenceNames.containsAll(readsSequenceNames)) {
StringBuilder warning = new StringBuilder();
warning.append("Limited overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference. Perhaps you're using the wrong reference?\n");
warning.append(System.getProperty("line.separator"));
warning.append(String.format("Reads contigs: %s%n", prettyPrintSequenceRecords(readsDictionary)));
warning.append(String.format("Reference contigs: %s%n", prettyPrintSequenceRecords(referenceDictionary)));
logger.warn(warning.toString());
}
}
private String prettyPrintSequenceRecords( SAMSequenceDictionary sequenceDictionary ) {
String[] sequenceRecordNames = new String[ sequenceDictionary.size() ];
int sequenceRecordIndex = 0;
for( SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences() )
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
return Arrays.deepToString(sequenceRecordNames);
}
/**
* Convenience function that binds RODs using the old-style command line parser to the new style list for
* a uniform processing.
@ -532,8 +610,8 @@ public class GenomeAnalysisEngine {
return outputTracker;
}
public TraversalEngine getEngine() {
return this.engine;
public SAMFileHeader getSAMFileHeader() {
return readsDataSource.getHeader();
}
/**
@ -542,7 +620,7 @@ public class GenomeAnalysisEngine {
* @return
*/
public SAMDataSource getDataSource() {
return this.dataSource;
return this.readsDataSource;
}
/**

6
java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
View File

@ -95,11 +95,15 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
}
}
public Object execute( Walker walker, ShardStrategy shardStrategy ) {
public Object execute( Walker walker, ShardStrategy shardStrategy, int maxIterations ) {
// Fast fail for walkers not supporting TreeReducible interface.
if (!( walker instanceof TreeReducible ))
throw new IllegalArgumentException("Hierarchical microscheduler only works with TreeReducible walkers");
// Having maxiterations in the execute method is a holdover from the old TraversalEngine days.
// Lets do something else with this.
traversalEngine.setMaximumIterations(maxIterations);
ReduceTree reduceTree = new ReduceTree(this);
walker.initialize();

10
java/src/org/broadinstitute/sting/gatk/executive/LinearMicroScheduler.java
View File

@ -6,10 +6,6 @@ import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
import org.broadinstitute.sting.gatk.Reads;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.util.Collection;
@ -35,7 +31,11 @@ public class LinearMicroScheduler extends MicroScheduler {
* @param walker Computation to perform over dataset.
* @param shardStrategy A strategy for sharding the data.
*/
public Object execute(Walker walker, ShardStrategy shardStrategy) {
public Object execute(Walker walker, ShardStrategy shardStrategy, int maxIterations) {
// Having maxiterations in the execute method is a holdover from the old TraversalEngine days.
// Lets do something else with this.
traversalEngine.setMaximumIterations(maxIterations);
walker.initialize();
Accumulator accumulator = Accumulator.create(walker);

95
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
View File

@ -25,9 +25,6 @@
package org.broadinstitute.sting.gatk.executive;
import net.sf.picard.reference.ReferenceSequenceFile;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
@ -36,7 +33,6 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
import java.util.*;
@ -91,6 +87,10 @@ public abstract class MicroScheduler {
* @param rods the rods to include in the traversal
*/
protected MicroScheduler(Walker walker, SAMDataSource reads, IndexedFastaSequenceFile reference, Collection<ReferenceOrderedDataSource> rods) {
this.reads = reads;
this.reference = reference;
this.rods = rods;
if (walker instanceof ReadWalker) {
traversalEngine = new TraverseReads();
} else if (walker instanceof LocusWalker) {
@ -101,30 +101,11 @@ public abstract class MicroScheduler {
traversalEngine = new TraverseDuplicates();
} else {
throw new UnsupportedOperationException("Unable to determine traversal type, the walker is an unknown type.");
}
this.reads = reads;
this.reference = reference;
this.rods = rods;
}
validate(this.reads,this.reference);
// Side effect: initialize the traversal engine with reads data.
// TODO: Give users a dedicated way of getting the header so that the MicroScheduler
// doesn't have to bend over backward providing legacy getters and setters.
traversalEngine.setSAMHeader(reads.getHeader());
traversalEngine.initialize();
}
/**
* A temporary getter for the traversal engine. In the future, clients
* of the microscheduler shouldn't need to know anything about the traversal engine.
*
* @return The traversal engine.
*/
public TraversalEngine getTraversalEngine() {
return traversalEngine;
}
/**
* Walks a walker over the given list of intervals.
*
@ -133,7 +114,7 @@ public abstract class MicroScheduler {
*
* @return the return type of the walker
*/
public abstract Object execute(Walker walker, ShardStrategy shardStrategy);
public abstract Object execute(Walker walker, ShardStrategy shardStrategy, int iterations );
/**
@ -174,68 +155,4 @@ public abstract class MicroScheduler {
* @return The reference maintained by this scheduler.
*/
public IndexedFastaSequenceFile getReference() { return reference; }
/**
* Now that all files are open, validate the sequence dictionaries of the reads vs. the reference.
* TODO: Doing this in the MicroScheduler is a bit late, but this is where data sources are initialized.
* TODO: Move the initialization of data sources back to the GenomeAnalysisEngine.
* @param reads Reads data source.
* @param reference Reference data source.
*/
private void validate( SAMDataSource reads, ReferenceSequenceFile reference ) {
if( reads == null || reference == null )
return;
// Compile a set of sequence names that exist in the BAM files.
SAMSequenceDictionary readsDictionary = reads.getHeader().getSequenceDictionary();
Set<String> readsSequenceNames = new TreeSet<String>();
for( SAMSequenceRecord dictionaryEntry: readsDictionary.getSequences() )
readsSequenceNames.add(dictionaryEntry.getSequenceName());
// Compile a set of sequence names that exist in the reference file.
SAMSequenceDictionary referenceDictionary = reference.getSequenceDictionary();
Set<String> referenceSequenceNames = new TreeSet<String>();
for( SAMSequenceRecord dictionaryEntry: referenceDictionary.getSequences() )
referenceSequenceNames.add(dictionaryEntry.getSequenceName());
if( readsSequenceNames.size() == 0 ) {
logger.info("Reads file is unmapped. Skipping validation against reference.");
return;
}
// If there's no overlap between reads and reference, data will be bogus. Throw an exception.
Set<String> intersectingSequenceNames = new HashSet<String>(readsSequenceNames);
intersectingSequenceNames.retainAll(referenceSequenceNames);
if( intersectingSequenceNames.size() == 0 ) {
StringBuilder error = new StringBuilder();
error.append("No overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference. Perhaps you're using the wrong reference?\n");
error.append(System.getProperty("line.separator"));
error.append(String.format("Reads contigs: %s%n", prettyPrintSequenceRecords(readsDictionary)));
error.append(String.format("Reference contigs: %s%n", prettyPrintSequenceRecords(referenceDictionary)));
logger.error(error.toString());
Utils.scareUser("No overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference.");
}
// If the two datasets are not equal and neither is a strict subset of the other, warn the user.
if( !readsSequenceNames.equals(referenceSequenceNames) &&
!readsSequenceNames.containsAll(referenceSequenceNames) &&
!referenceSequenceNames.containsAll(readsSequenceNames)) {
StringBuilder warning = new StringBuilder();
warning.append("Limited overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference. Perhaps you're using the wrong reference?\n");
warning.append(System.getProperty("line.separator"));
warning.append(String.format("Reads contigs: %s%n", prettyPrintSequenceRecords(readsDictionary)));
warning.append(String.format("Reference contigs: %s%n", prettyPrintSequenceRecords(referenceDictionary)));
logger.warn(warning.toString());
}
}
private String prettyPrintSequenceRecords( SAMSequenceDictionary sequenceDictionary ) {
String[] sequenceRecordNames = new String[ sequenceDictionary.size() ];
int sequenceRecordIndex = 0;
for( SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences() )
sequenceRecordNames[sequenceRecordIndex++] = sequenceRecord.getSequenceName();
return Arrays.deepToString(sequenceRecordNames);
}
}

26
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
View File

@ -1,10 +1,8 @@
package org.broadinstitute.sting.gatk.traversals;
import net.sf.samtools.SAMFileHeader;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.datasources.shards.Shard;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.GenomeLoc;
@ -20,9 +18,6 @@ public abstract class TraversalEngine {
// Maximum number of reads to process before finishing
protected long maximumIterations = -1;
// the stored header
private SAMFileHeader myHeader = null;
/** our log, which we want to capture anything from this class */
protected static Logger logger = Logger.getLogger(TraversalEngine.class);
@ -34,27 +29,6 @@ public abstract class TraversalEngine {
this.maximumIterations = maximumIterations;
}
/**
* get the associated SAM header for our run
*
* @return the header if it's stored, null if not
*/
public SAMFileHeader getSAMHeader() {
return myHeader;
}
/**
* set's the SAM header for this traversal, which should
* be the merged header in the multiple BAM file case.
*
* @param myHeader the passed in header
*/
public void setSAMHeader(SAMFileHeader myHeader) {
this.myHeader = myHeader;
}
/**
* @param curTime (current runtime, in millisecs)
*

2
java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
View File

@ -75,7 +75,7 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
if ( platform != null ) {
Object readGroupAttr = read.getAttribute("RG");
if ( readGroupAttr != null ) {
SAMReadGroupRecord readGroup = getToolkit().getEngine().getSAMHeader().getReadGroup(readGroupAttr.toString());
SAMReadGroupRecord readGroup = getToolkit().getSAMFileHeader().getReadGroup(readGroupAttr.toString());
if ( readGroup != null ) {
Object readPlatformAttr = readGroup.getAttribute("PL");
if ( readPlatformAttr != null )

13
java/src/org/broadinstitute/sting/gatk/walkers/SplitSamFileWalker.java
View File

@ -26,20 +26,11 @@
package org.broadinstitute.sting.gatk.walkers;
import net.sf.samtools.*;
import org.broadinstitute.sting.gatk.walkers.WalkerName;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Requires;
import org.broadinstitute.sting.gatk.walkers.DataSource;
import org.broadinstitute.sting.gatk.walkers.recalibration.*;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.utils.*;
import org.apache.log4j.Logger;
import java.util.*;
import java.util.regex.Pattern;
import java.util.regex.Matcher;
import java.io.File;
import java.io.FileNotFoundException;
@WalkerName("SplitSamFile")
@Requires({DataSource.READS})
@ -74,10 +65,10 @@ public class SplitSamFileWalker extends ReadWalker<SAMRecord, Map<String, SAMFil
public Map<String, SAMFileWriter> reduceInit() {
HashMap<String, SAMFileHeader> headers = new HashMap<String, SAMFileHeader>();
for ( SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) {
for ( SAMReadGroupRecord readGroup : this.getToolkit().getSAMFileHeader().getReadGroups()) {
final String sample = readGroup.getSample();
if ( ! headers.containsKey(sample) ) {
SAMFileHeader header = Utils.copySAMFileHeader(this.getToolkit().getEngine().getSAMHeader());
SAMFileHeader header = Utils.copySAMFileHeader(this.getToolkit().getSAMFileHeader());
logger.debug(String.format("Creating BAM header for sample %s", sample));
ArrayList<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
header.setReadGroups(readGroups);

5
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
View File

@ -61,7 +61,6 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )
throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1");
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
if ( writer != null ) {
readsToWrite = new TreeSet<ComparableSAMRecord>();
}
@ -888,7 +887,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
String reference = "AAAAAACCCCCCAAAAAA";
// the alternate reference is: "AAAAAACCCTTCCCAAAAAA";
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
SAMFileHeader header = getToolkit().getSAMFileHeader();
SAMRecord r1 = new SAMRecord(header);
r1.setReadName("1");
r1.setReadString("AACCCCCC");
@ -938,7 +937,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
String reference = "AAAAAACCCTTCCCAAAAAA";
// the alternate reference is: "AAAAAACCCCCCAAAAAA";
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>();
SAMFileHeader header = getToolkit().getEngine().getSAMHeader();
SAMFileHeader header = getToolkit().getSAMFileHeader();
SAMRecord r1 = new SAMRecord(header);
r1.setReadName("1");
r1.setReadString("ACCCTTCC");

2
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
View File

@ -50,7 +50,7 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
*/
public void initialize() {
Set<String> readGroups = new HashSet<String>();
for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) {
for (SAMReadGroupRecord readGroup : this.getToolkit().getSAMFileHeader().getReadGroups()) {
if( readGroup.getAttribute("PL") == null )
Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are supported",readGroup.getReadGroupId()));
if( !isSupportedReadGroup(readGroup) )

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/CoverageBySample.java
View File

@ -25,7 +25,7 @@ public class CoverageBySample extends LocusWalker<String, String>
public void initialize()
{
GenomeAnalysisEngine toolkit = this.getToolkit();
this.header = toolkit.getEngine().getSAMHeader();
this.header = toolkit.getSAMFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
sample_names = new ArrayList<String>();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/IOCrusherWalker.java
View File

@ -53,7 +53,7 @@ public class IOCrusherWalker extends ReadWalker<SAMRecord, ArrayList<SAMFileWrit
public ArrayList<SAMFileWriter> reduceInit() {
ArrayList<SAMFileWriter> outputs = new ArrayList<SAMFileWriter>(nWaysOut);
for ( int i = 0; i < nWaysOut; i++ ) {
SAMFileHeader header = this.getToolkit().getEngine().getSAMHeader();
SAMFileHeader header = this.getToolkit().getSAMFileHeader();
outputs.add(Utils.createSAMFileWriterWithCompression(header, true, outputBase + "." + i + ".bam", BAMcompression));
}
return outputs;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/ListSampleIds.java
View File

@ -16,7 +16,7 @@ public class ListSampleIds extends LocusWalker<Boolean, Boolean>
public void initialize()
{
GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getEngine().getSAMHeader();
SAMFileHeader header = toolkit.getSAMFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
for (int i = 0; i < read_groups.size(); i++)

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/MultiSampleCaller.java
View File

@ -90,7 +90,7 @@ public class MultiSampleCaller extends LocusWalker<MultiSampleCaller.MultiSample
GenomeAnalysisEngine toolkit = this.getToolkit();
this.header = toolkit.getEngine().getSAMHeader();
this.header = toolkit.getSAMFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
sample_names = new ArrayList<String>();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/PoolCallingExperiment.java
View File

@ -34,7 +34,7 @@ public class PoolCallingExperiment extends LocusWalker<AlleleFrequencyEstimate,
public void initialize()
{
GenomeAnalysisEngine toolkit = this.getToolkit();
SAMFileHeader header = toolkit.getEngine().getSAMHeader();
SAMFileHeader header = toolkit.getSAMFileHeader();
List<SAMReadGroupRecord> read_groups = header.getReadGroups();
sample_names = new ArrayList<String>();

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/SingleSampleGenotyper.java
View File

@ -259,7 +259,7 @@ public class SingleSampleGenotyper extends LocusWalker<GenotypeCall, GenotypeWri
* @return an empty string
*/
public GenotypeWriter reduceInit() {
return GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getEngine().getSAMHeader(), VARIANTS_FILE);
return GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE);
}