From 16777e387527d8d2a63ce59f8de3383c63b118ef Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 12 Jan 2010 18:47:43 +0000
Subject: [PATCH] more fixes for the empty interval list problem; you can now
 run LocusWindow traversals with an empty interval list, but the GATK will
 give you a warning (unless you're running in unsafe mode).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java      |  5 +++--
 .../shards/IntervalShardStrategy.java         | 19 ++-----------------
 .../shards/IntervalShardStrategyTest.java     |  4 ++--
 3 files changed, 7 insertions(+), 21 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index d6d0528ea..10ef3d375 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -626,8 +626,9 @@ public class GenomeAnalysisEngine {
                         SHARD_SIZE, maxIterations);
             }
         } else if (walker instanceof LocusWindowWalker) {
-            if (intervals == null || intervals.isEmpty())
-                throw new StingException("Unable to shard: walker is of type LocusWindow, but no intervals were provided");
+            if ((intervals == null || intervals.isEmpty()) && !this.argCollection.unsafe)
+                Utils.warnUser("walker is of type LocusWindow (which operates over intervals), but no intervals were provided." +
+                               "This may be unintentional, check your command-line arguments.");
             shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.INTERVAL,
                     drivingDataSource.getSequenceDictionary(),
                     SHARD_SIZE,
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java
index 1cc1eb34d..51d18f728 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategy.java
@@ -57,7 +57,7 @@ public class IntervalShardStrategy implements ShardStrategy {
      * @param size the next recommended shard size.
      */
     public void adjustNextShardSize( long size ) {
-        this.size = size;
+        this.size = size; // we don't do anything with the size in this case, but we should store it anyway
     }
 
     /**
@@ -67,26 +67,11 @@ public class IntervalShardStrategy implements ShardStrategy {
      * @param locations
      */
     IntervalShardStrategy( long size, GenomeLocSortedSet locations, Shard.ShardType shardType ) {
-        if (locations == null || locations.isEmpty()) {
-            throw new StingException("IntervalShardStrategy: genomic regions list is empty.");
-        }
         type = shardType;
-        this.regions = locations.clone();
+        this.regions = locations == null ? new GenomeLocSortedSet() : locations.clone();
         this.size = size;
     }
 
-    /**
-     * the default constructor
-     *
-     * @param dict the sequence dictionary to use
-     */
-    IntervalShardStrategy( SAMSequenceDictionary dict, GenomeLocSortedSet locations ) {
-        if (locations == null || locations.isEmpty()) {
-            throw new StingException("IntervalShardStrategy: genomic regions list is empty.");
-        }
-        this.regions = locations.clone();
-    }
-
     /**
      * returns true if there are additional shards
      *
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java
index cca28ad85..e94a4d908 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java
@@ -65,8 +65,8 @@ public class IntervalShardStrategyTest extends BaseTest {
         mSortedSet = new GenomeLocSortedSet();
     }
 
-    @Test(expected = StingException.class)
-    public void testExceptionOnEmpty() {
+    @Test
+    public void testNoExceptionOnEmpty() {
         IntervalShardStrategy strat = new IntervalShardStrategy(100, mSortedSet,Shard.ShardType.LOCUS_INTERVAL);
     }