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RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.

This commit is contained in:
Eric Banks 2011-10-06 15:57:49 -04:00
parent 1b0735f0a3
commit 6eb87bf58a
2 changed files with 34 additions and 30 deletions
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60
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
View File

@ -50,6 +50,7 @@ import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.TreeSet;
/**
* Emits intervals for the Local Indel Realigner to target for realignment.
@ -253,9 +254,12 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
public void onTraversalDone(EventPair sum) {
if ( sum.left != null && sum.left.isReportableEvent() )
out.println(sum.left.toString());
sum.intervals.add(sum.left.getLoc());
if ( sum.right != null && sum.right.isReportableEvent() )
out.println(sum.right.toString());
sum.intervals.add(sum.right.getLoc());
for ( GenomeLoc loc : sum.intervals )
out.println(loc);
}
public EventPair reduceInit() {
@ -272,39 +276,39 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
} else if ( lhs.right == null ) {
if ( rhs.right == null ) {
if ( canBeMerged(lhs.left, rhs.left) )
result = new EventPair(mergeEvents(lhs.left, rhs.left), null);
result = new EventPair(mergeEvents(lhs.left, rhs.left), null, lhs.intervals, rhs.intervals);
else
result = new EventPair(lhs.left, rhs.left);
result = new EventPair(lhs.left, rhs.left, lhs.intervals, rhs.intervals);
} else {
if ( canBeMerged(lhs.left, rhs.left) )
result = new EventPair(mergeEvents(lhs.left, rhs.left), rhs.right);
result = new EventPair(mergeEvents(lhs.left, rhs.left), rhs.right, lhs.intervals, rhs.intervals);
else {
if ( rhs.left.isReportableEvent() )
out.println(rhs.left.toString());
result = new EventPair(lhs.left, rhs.right);
rhs.intervals.add(rhs.left.getLoc());
result = new EventPair(lhs.left, rhs.right, lhs.intervals, rhs.intervals);
}
}
} else if ( rhs.right == null ) {
if ( canBeMerged(lhs.right, rhs.left) )
result = new EventPair(lhs.left, mergeEvents(lhs.right, rhs.left));
result = new EventPair(lhs.left, mergeEvents(lhs.right, rhs.left), lhs.intervals, rhs.intervals);
else {
if ( lhs.right.isReportableEvent() )
out.println(lhs.right.toString());
result = new EventPair(lhs.left, rhs.left);
lhs.intervals.add(lhs.right.getLoc());
result = new EventPair(lhs.left, rhs.left, lhs.intervals, rhs.intervals);
}
} else {
if ( canBeMerged(lhs.right, rhs.left) ) {
Event merge = mergeEvents(lhs.right, rhs.left);
if ( merge.isReportableEvent() )
out.println(merge.toString());
lhs.intervals.add(merge.getLoc());
} else {
if ( lhs.right.isReportableEvent() )
out.println(lhs.right.toString());
lhs.intervals.add(lhs.right.getLoc());
if ( rhs.left.isReportableEvent() )
out.println(rhs.left.toString());
rhs.intervals.add(rhs.left.getLoc());
}
result = new EventPair(lhs.left, rhs.right);
result = new EventPair(lhs.left, rhs.right, lhs.intervals, rhs.intervals);
}
return result;
@ -318,22 +322,14 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
} else if ( sum.right == null ) {
if ( canBeMerged(sum.left, value) )
sum.left = mergeEvents(sum.left, value);
// While ideally we shouldn't do anything differently depending on the number of threads, there is a practical reason for doing so:
// if we know that we are single-threaded then we can ensure that the intervals are emitted in order, which leads to a large
// performance improvement (esp. memory) in the IndelRealigner (because we don't have to store all of the intervals in memory to sort them).
else if ( getToolkit().getArguments().numberOfThreads > 1 )
else
sum.right = value;
else {
if ( sum.left.isReportableEvent() )
out.println(sum.left.toString());
sum.left = value;
}
} else {
if ( canBeMerged(sum.right, value) )
sum.right = mergeEvents(sum.right, value);
else {
if ( sum.right.isReportableEvent() )
out.println(sum.right.toString());
sum.intervals.add(sum.right.getLoc());
sum.right = value;
}
}
@ -355,18 +351,26 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
class EventPair {
public Event left, right;
public TreeSet<GenomeLoc> intervals = new TreeSet<GenomeLoc>();
public EventPair(Event left, Event right) {
this.left = left;
this.right = right;
}
public EventPair(Event left, Event right, TreeSet<GenomeLoc> set1, TreeSet<GenomeLoc> set2) {
this.left = left;
this.right = right;
intervals.addAll(set1);
intervals.addAll(set2);
}
}
class Event {
public int furthestStopPos;
public GenomeLoc loc;
public int eventStartPos;
private GenomeLoc loc;
private int eventStartPos;
private int eventStopPos;
private EVENT_TYPE type;
private ArrayList<Integer> pointEvents = new ArrayList<Integer>();
@ -421,8 +425,8 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
return getToolkit().getGenomeLocParser().isValidGenomeLoc(loc.getContig(), eventStartPos, eventStopPos, true) && eventStopPos >= 0 && eventStopPos - eventStartPos < maxIntervalSize;
}
public String toString() {
return String.format("%s:%d-%d", loc.getContig(), eventStartPos, eventStopPos);
public GenomeLoc getLoc() {
return getToolkit().getGenomeLocParser().createGenomeLoc(loc.getContig(), eventStartPos, eventStopPos);
}
}
}

4
public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -13,13 +13,13 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam --mismatchFraction 0.15 -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("e7accfa58415d6da80383953b1a3a986"));
Arrays.asList("3f0b63a393104d0c4158c7d1538153b8"));
executeTest("test standard", spec1);
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator --known " + b36dbSNP129 + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s",
1,
Arrays.asList("0367d39a122c8ac0899fb868a82ef728"));
Arrays.asList("5085054c78e256432dc75c85a9ac631c"));
executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(