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Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@191 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-25 16:01:58 +00:00
parent c18f8fbf5f
commit d457778283
2 changed files with 27 additions and 42 deletions
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3
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -185,10 +185,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
// Try to get the walker specified // Try to get the walker specified
try { try {
LocusWalker<?, ?> walker = (LocusWalker<?, ?>) my_walker; LocusWalker<?, ?> walker = (LocusWalker<?, ?>) my_walker;
if ( INTERVALS_FILE == null )
engine.traverseByLoci(walker); engine.traverseByLoci(walker);
else
engine.traverseByLociByInterval(walker);
} }
catch (java.lang.ClassCastException e) { catch (java.lang.ClassCastException e) {
// I guess we're a read walker LOL // I guess we're a read walker LOL

60
java/src/org/broadinstitute/sting/gatk/TraversalEngine.java
View File

@ -244,6 +244,10 @@ public class TraversalEngine {
} }
} }
public boolean hasLocations() {
return this.locs != null;
}
/** /**
* Returns true iff we have a specified series of locations to process AND we are past the last * Returns true iff we have a specified series of locations to process AND we are past the last
* location in the list. It means that, in a serial processing of the genome, that we are done. * location in the list. It means that, in a serial processing of the genome, that we are done.
@ -551,15 +555,33 @@ public class TraversalEngine {
* @return 0 on success * @return 0 on success
*/ */
protected <M, T> int traverseByLoci(LocusWalker<M, T> walker) { protected <M, T> int traverseByLoci(LocusWalker<M, T> walker) {
samReadIter = initializeReads(); samReader = initializeSAMFile(readsFile);
verifySortOrder(true); verifySortOrder(true);
// initialize the walker object // initialize the walker object
walker.initialize(); walker.initialize();
T sum = walker.reduceInit();
if ( samReader.hasIndex() && hasLocations() ) {
// we are doing interval-based traversals
for ( GenomeLoc interval : locs ) {
logger.debug(String.format("Processing locus %s", interval.toString()));
CloseableIterator<SAMRecord> readIter = samReader.queryOverlapping( interval.getContig(),
(int)interval.getStart(),
(int)interval.getStop() );
Iterator<SAMRecord> wrappedIter = WrapReadsIterator( readIter, false );
sum = carryWalkerOverInterval(walker, wrappedIter, sum, interval);
readIter.close();
}
}
else {
// We aren't locus oriented // We aren't locus oriented
T sum = carryWalkerOverInterval(walker, samReadIter, walker.reduceInit(), null); samReadIter = WrapReadsIterator(getReadsIterator(samReader), true);
sum = carryWalkerOverInterval(walker, samReadIter, sum, null);
}
printOnTraversalDone("loci", sum); printOnTraversalDone("loci", sum);
walker.onTraversalDone(); walker.onTraversalDone();
@ -617,40 +639,6 @@ public class TraversalEngine {
return sum; return sum;
} }
/**
* Same as the normal locus traverser, but oriented by locus, rather than implicitly
*
* @param walker A locus walker object
* @param <M> MapType -- the result of calling map() on walker
* @param <T> ReduceType -- the result of calling reduce() on the walker
* @return 0 on success
*/
protected <M, T> int traverseByLociByInterval(LocusWalker<M, T> walker) {
//verifySortOrder(true);
// initialize the walker object
walker.initialize();
// Initialize the T sum using the walker
T sum = walker.reduceInit();
samReader = initializeSAMFile(readsFile);
for ( GenomeLoc interval : locs ) {
logger.debug(String.format("Processing locus %s", interval.toString()));
CloseableIterator<SAMRecord> readIter = samReader.queryOverlapping( interval.getContig(),
(int)interval.getStart(),
(int)interval.getStop() );
Iterator<SAMRecord> wrappedIter = WrapReadsIterator( readIter, false );
sum = carryWalkerOverInterval(walker, wrappedIter, sum, interval);
readIter.close();
}
printOnTraversalDone("loci", sum);
walker.onTraversalDone();
return 0;
}
/** /**
* Traverse by read -- the key driver of linearly ordered traversal of reads. Provides a single read to * Traverse by read -- the key driver of linearly ordered traversal of reads. Provides a single read to
* the walker object, in coordinate order. Supports all of the * the walker object, in coordinate order. Supports all of the