From ee22c1bf448e60eeb9dd122126699a364714fe18 Mon Sep 17 00:00:00 2001
From: Joel Thibault <thibault@broadinstitute.org>
Date: Tue, 18 Dec 2012 18:45:36 -0500
Subject: [PATCH] More TODOs

---
 .../sting/gatk/traversals/TraverseActiveRegionsTest.java   | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
index 173113615..185eca85c 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegionsTest.java
@@ -112,6 +112,13 @@ public class TraverseActiveRegionsTest extends BaseTest {
         genomeLocParser = new GenomeLocParser(dictionary);
 
         // TODO: test shard boundaries
+        // TODO: reads with indels
+        // TODO: reads which span many regions
+        // TODO: reads which are partially between intervals (in/outside extension)
+        // TODO: duplicate reads
+
+        // TODO: should we assign reads which are completely outside intervals but within extension?
+
 
         intervals = new ArrayList<GenomeLoc>();
         intervals.add(genomeLocParser.createGenomeLoc("1", 10, 20));