From 4faa680887875a0239acd69901fcf5d557d052a6 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 2 Apr 2009 20:19:39 +0000
Subject: [PATCH] *Massive* speed-up for interval-based by-read traversals.
 [Could do more optimizing, but this simple fix was good enough for now]

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@266 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/traversals/TraverseByReads.java      |  2 ++
 .../broadinstitute/sting/utils/GenomeLoc.java | 20 +++++++++++++++++--
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
index 0d70379d7..639ad5407 100644
--- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
+++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
@@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.FastaSequenceFile2;
 
 import java.util.List;
 import java.util.Arrays;
@@ -52,6 +53,7 @@ public class TraverseByReads extends TraversalEngine {
      */
     public <M, T> Object traverseByRead(ReadWalker<M, T> walker, ArrayList<GenomeLoc> locations) {
         samReadIter = initializeReads();
+        GenomeLoc.setupRefContigOrdering(new FastaSequenceFile2(refFileName));
 
         if (refFileName == null && !walker.requiresOrderedReads() && verifyingSamReadIter != null) {
             logger.warn(String.format("STATUS: No reference file provided and unordered reads are tolerated, enabling out of order read processing."));
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 5e1c7869b..8a6d86621 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -41,6 +41,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
     //public static Map<String, Integer> refContigOrdering = null;
     private static SAMSequenceDictionary contigInfo = null;
     private static HashMap<String, String> interns = null;
+    private static int lastGoodIntervalIndex = 0;
 
     public static boolean hasKnownContigOrdering() {
         return contigInfo != null;
@@ -271,10 +272,24 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
         if ( locs.size() == 0 ) {
             return true;
         } else {
-            for ( GenomeLoc loc : locs ) {
+            for ( int i = lastGoodIntervalIndex; i < locs.size(); i++ ) {
+                GenomeLoc loc = locs.get(i);
+                // since it's ordered, we can do some simple checks to save us tons of time
+                if ( hasKnownContigOrdering() ) {
+                    int curIndex = getContigIndex(curr.contig);
+                    int locIndex = getContigIndex(loc.contig);
+                    // skip loci before intervals begin
+                    if (curIndex < locIndex)
+                        return false;
+                    // skip loci between intervals
+                    if (curIndex == locIndex && curr.stop < loc.start)
+                        return false;
+                }
                 //System.out.printf("  Overlap %s vs. %s => %b%n", loc, curr, loc.overlapsP(curr));
-                if (loc.overlapsP(curr))
+                if (loc.overlapsP(curr)) {
+                    lastGoodIntervalIndex = i;
                     return true;
+                }
             }
             return false;
         }
@@ -403,6 +418,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
             int thisIndex = getContigIndex(thisContig);
             int thatIndex = getContigIndex(thatContig);
 
+
             if ( thisIndex == -1 )
             {
                 if ( thatIndex == -1 )