From 362929187e1652b7a70a7eeb245d7947dcaf867e Mon Sep 17 00:00:00 2001
From: Nils Homer <nilshomer@gmail.com>
Date: Wed, 27 Apr 2016 20:15:37 -0400
Subject: [PATCH] Provide a method that for each source contig gives the set of
 destination contigs used in liftover.

---
 .../htsjdk/samtools/liftover/LiftOver.java    | 27 +++++++++++++++++++
 .../samtools/liftover/LiftOverTest.java       | 10 +++++++
 2 files changed, 37 insertions(+)

diff --git a/src/main/java/htsjdk/samtools/liftover/LiftOver.java b/src/main/java/htsjdk/samtools/liftover/LiftOver.java
index deb9067c1c..e422a72198 100644
--- a/src/main/java/htsjdk/samtools/liftover/LiftOver.java
+++ b/src/main/java/htsjdk/samtools/liftover/LiftOver.java
@@ -32,7 +32,12 @@
 
 import java.io.File;
 import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 /**
  * Java port of UCSC liftOver.  Only the most basic liftOver functionality is implemented.
@@ -47,6 +52,7 @@ public class LiftOver {
 
     private double liftOverMinMatch = DEFAULT_LIFTOVER_MINMATCH;
     private final OverlapDetector<Chain> chains;
+    private final Map<String, Set<String>> contigMap = new HashMap<>();
 
     /**
      * Load UCSC chain file in order to lift over Intervals.
@@ -54,6 +60,20 @@ public class LiftOver {
     public LiftOver(File chainFile) {
         IOUtil.assertFileIsReadable(chainFile);
         chains = Chain.loadChains(chainFile);
+
+        for (final Chain chain : this.chains.getAll()) {
+            final String from = chain.fromSequenceName;
+            final String to   = chain.toSequenceName;
+            final Set<String> names;
+            if (contigMap.containsKey(from)) {
+                names = contigMap.get(from);
+            }
+            else {
+                names = new HashSet<>();
+                contigMap.put(from, names);
+            }
+            names.add(to);
+        }
     }
 
     /**
@@ -139,6 +159,13 @@ public List<PartialLiftover> diagnosticLiftover(final Interval interval) {
         return ret;
     }
 
+    /**
+     * @return the set of destination contigs for each source contig in the chains file.
+     */
+    public Map<String, Set<String>> getContigMap() {
+        return Collections.unmodifiableMap(contigMap);
+    }
+
     private static Interval createToInterval(final String intervalName, final boolean sourceNegativeStrand, final TargetIntersection targetIntersection) {
         // Compute the query interval given the offsets of the target interval start and end into the first and
         // last ContinuousBlocks.
diff --git a/src/test/java/htsjdk/samtools/liftover/LiftOverTest.java b/src/test/java/htsjdk/samtools/liftover/LiftOverTest.java
index 01aaf9b2f3..8e9f92e6f2 100644
--- a/src/test/java/htsjdk/samtools/liftover/LiftOverTest.java
+++ b/src/test/java/htsjdk/samtools/liftover/LiftOverTest.java
@@ -34,6 +34,7 @@
 import java.io.PrintWriter;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 import java.util.TreeMap;
 
 /**
@@ -44,10 +45,12 @@ public class LiftOverTest {
     private static final File CHAIN_FILE = new File(TEST_DATA_DIR, "hg18ToHg19.over.chain");
 
     private LiftOver liftOver;
+    Map<String, Set<String>> contigMap;
 
     @BeforeClass
     public void initLiftOver() {
         liftOver = new LiftOver(CHAIN_FILE);
+        contigMap = liftOver.getContigMap();
     }
 
     @Test(dataProvider = "testIntervals")
@@ -455,4 +458,11 @@ public void testWriteChain() throws Exception {
         }
         Assert.assertEquals(newChainMap, originalChainMap);
     }
+
+    @Test(dataProvider = "testIntervals")
+    public void testGetContigMap(final Interval in, final Interval expected) {
+        if (expected != null) {
+            Assert.assertTrue(contigMap.get(in.getContig()).contains(expected.getContig()));
+        }
+    }
 }