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remove hacked traversal in preparation for move to Matt's new one 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1091 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-25 14:32:05 +00:00
parent 940d75171a
commit 347608cfe0
2 changed files with 5 additions and 137 deletions
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132
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java
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@ -76,10 +76,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
if ( !samReader.hasIndex() )
Utils.scareUser("Processing locations were requested, but no index was found for the input SAM/BAM file. This operation is potentially dangerously slow, aborting.");
if ( walker.actOnNonIntervalReads() )
sum = fullInputTraversal(walker, locations, sum);
else
sum = strictIntervalTraversal(walker, locations, sum);
sum = intervalTraversal(walker, locations, sum);
}
//printOnTraversalDone("intervals", sum);
@ -87,8 +84,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
return sum;
}
protected <M, T> T strictIntervalTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
LocusContext nextLocusToCarry = null;
protected <M, T> T intervalTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
for ( GenomeLoc interval : locations ) {
logger.debug(String.format("Processing interval %s", interval.toString()));
@ -97,129 +93,9 @@ public class TraverseByLocusWindows extends TraversalEngine {
LocusContext locus = getLocusContext(wrappedIter, interval);
readIter.close();
if ( nextLocusToCarry == null ) {
nextLocusToCarry = locus;
} else if ( nextLocusToCarry.getLocation().overlapsP(locus.getLocation()) ) {
nextLocusToCarry = merge(nextLocusToCarry, locus);
} else {
sum = carryWalkerOverInterval(walker, sum, nextLocusToCarry);
nextLocusToCarry = locus;
}
//sum = carryWalkerOverInterval(walker, sum, locus);
System.out.println(locus.getLocation());
}
if ( nextLocusToCarry != null )
sum = carryWalkerOverInterval(walker, sum, nextLocusToCarry);
return sum;
}
protected <M, T> T fullInputTraversal(LocusWindowWalker<M, T> walker, List<GenomeLoc> locations, T sum) {
ArrayList<LocusContext> nextLociToCarry = new ArrayList<LocusContext>();
// set everything up
GenomeLoc currentInterval = (locations.size() > 0 ? locations.get(0) : null);
int locationsIndex = 0;
ArrayList<SAMRecord> intervalReads = new ArrayList<SAMRecord>();
Iterator<SAMRecord> readIter = getIteratorOverDesiredRegion(samReader,null);
while (readIter.hasNext()) {
TraversalStatistics.nRecords++;
SAMRecord read = readIter.next();
// apparently, unmapped reads can occur anywhere in the file!
if ( read.getReadUnmappedFlag() ) {
walker.nonIntervalReadAction(read);
continue;
}
// if there are no locations or we're past the last one, then act on the read separately
if ( currentInterval == null ) {
if ( nextLociToCarry.size() > 0 ) {
sum = carryWalkerOverInterval(walker, sum, nextLociToCarry.get(0));
for (int i=1; i < nextLociToCarry.size(); i++)
walker.nonIntervalReadAction(nextLociToCarry.get(i).getReads().get(0));
nextLociToCarry.clear();
}
walker.nonIntervalReadAction(read);
}
else {
GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
// if we're in the current interval, add it to the list
if ( currentInterval.overlapsP(loc) ) {
intervalReads.add(read);
}
// if we're not yet in the interval, act on the read separately
else if ( currentInterval.isPast(loc) ) {
if ( nextLociToCarry.size() == 0 ) {
walker.nonIntervalReadAction(read);
} else {
ArrayList<SAMRecord> list = new ArrayList<SAMRecord>();
list.add(read);
nextLociToCarry.add(new LocusContext(loc, list, null));
}
}
// otherwise, we're past the interval so first deal with the collected reads and then this one
else {
if ( intervalReads.size() > 0 ) {
Iterator<SAMRecord> wrappedIter = wrapReadsIterator(intervalReads.iterator(), false);
LocusContext locus = getLocusContext(wrappedIter, currentInterval);
if ( nextLociToCarry.size() == 0 ) {
nextLociToCarry.add(locus);
} else if ( nextLociToCarry.get(0).getLocation().overlapsP(locus.getLocation()) ) {
LocusContext newLocus = merge(nextLociToCarry.get(0), locus);
for (int i=1; i < nextLociToCarry.size(); i++)
newLocus = merge(newLocus, nextLociToCarry.get(i));
nextLociToCarry.clear();
nextLociToCarry.add(newLocus);
} else {
sum = carryWalkerOverInterval(walker, sum, nextLociToCarry.get(0));
for (int i=1; i < nextLociToCarry.size(); i++)
walker.nonIntervalReadAction(nextLociToCarry.get(i).getReads().get(0));
nextLociToCarry.clear();
nextLociToCarry.add(locus);
}
// then prepare for the next interval
intervalReads.clear();
}
currentInterval = (++locationsIndex < locations.size() ? locations.get(locationsIndex) : null);
if ( nextLociToCarry.size() == 0 ) {
walker.nonIntervalReadAction(read);
} else {
ArrayList<SAMRecord> list = new ArrayList<SAMRecord>();
list.add(read);
nextLociToCarry.add(new LocusContext(loc, list, null));
}
}
}
}
// some cleanup
if ( intervalReads.size() > 0 ) {
Iterator<SAMRecord> wrappedIter = wrapReadsIterator(intervalReads.iterator(), false);
LocusContext locus = getLocusContext(wrappedIter, currentInterval);
if ( nextLociToCarry.size() == 0 ) {
nextLociToCarry.add(locus);
} else if ( nextLociToCarry.get(0).getLocation().overlapsP(locus.getLocation()) ) {
LocusContext newLocus = merge(nextLociToCarry.get(0), locus);
for (int i=1; i < nextLociToCarry.size(); i++)
newLocus = merge(newLocus, nextLociToCarry.get(i));
nextLociToCarry.clear();
nextLociToCarry.add(newLocus);
} else {
sum = carryWalkerOverInterval(walker, sum, nextLociToCarry.get(0));
for (int i=1; i < nextLociToCarry.size(); i++)
walker.nonIntervalReadAction(nextLociToCarry.get(i).getReads().get(0));
nextLociToCarry.clear();
nextLociToCarry.add(locus);
}
}
if ( nextLociToCarry.size() > 0 ) {
sum = carryWalkerOverInterval(walker, sum, nextLociToCarry.get(0));
for (int i=1; i < nextLociToCarry.size(); i++)
walker.nonIntervalReadAction(nextLociToCarry.get(i).getReads().get(0));
}
return sum;
}

10
java/src/org/broadinstitute/sting/gatk/walkers/LocusWindowWalker.java
View File

@ -19,18 +19,10 @@ public abstract class LocusWindowWalker<MapType, ReduceType> extends Walker<MapT
return true; // We are keeping all the intervals
}
// do we care about reads that are not part of our intervals?
public boolean actOnNonIntervalReads() {
return false; // Don't act on them
}
// What do we do with the reads that are not part of our intervals?
public void nonIntervalReadAction(SAMRecord read) { }
// Map over the org.broadinstitute.sting.gatk.LocusContext
public abstract MapType map(RefMetaDataTracker tracker, String ref, LocusContext context);
// Given result of map function
public abstract ReduceType reduceInit();
public abstract ReduceType reduce(MapType value, ReduceType sum);
}
}