From 6eb87bf58a60e65abf89f7096ecbe06bef790ee4 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Thu, 6 Oct 2011 15:57:49 -0400
Subject: [PATCH] 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.

---
 .../indels/RealignerTargetCreator.java        | 60 ++++++++++---------
 ...RealignerTargetCreatorIntegrationTest.java |  4 +-
 2 files changed, 34 insertions(+), 30 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index e83667e8c..e1333b7f2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -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);
         }
     }
 }
\ No newline at end of file
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
index 1873ccbe2..fdb310428 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
@@ -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(