From 120f90da5b400826e99005ed9b3bc8d6afb0cab0 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 7 Jul 2010 03:14:59 +0000
Subject: [PATCH] Interval support for ref walkers while streaming.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3725 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java        | 17 ++++++++++++++---
 .../datasources/shards/MonolithicShard.java     |  9 ++++-----
 .../shards/MonolithicShardStrategy.java         |  5 +++--
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 7e5cb30a1..5e6c08e73 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -729,8 +729,10 @@ public class GenomeAnalysisEngine {
         // Use monolithic sharding if no index is present.  Monolithic sharding is always required for the original
         // sharding system; it's required with the new sharding system only for locus walkers.
         if(readsDataSource != null && !readsDataSource.hasIndex() ) { 
-            if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM) || intervals != null)
-                throw new StingException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM, or with unindexed BAM files with the -L option");
+            if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
+                throw new StingException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM");
+            if(intervals != null && WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE)
+                throw new StingException("Cannot shard input by interval when walker is not driven by reference.");
 
             Shard.ShardType shardType;
             if(walker instanceof LocusWalker) {
@@ -743,7 +745,16 @@ public class GenomeAnalysisEngine {
             else
                 throw new StingException("The GATK cannot currently process unindexed BAM files");
 
-            return new MonolithicShardStrategy(shardType,drivingDataSource.getSequenceDictionary());
+            List<GenomeLoc> region;
+            if(intervals != null)
+                region = intervals.toList();
+            else {
+                region = new ArrayList<GenomeLoc>();
+                for(SAMSequenceRecord sequenceRecord: drivingDataSource.getSequenceDictionary().getSequences())
+                    region.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));
+            }
+
+            return new MonolithicShardStrategy(shardType,region);
         }
 
         ShardStrategy shardStrategy = null;
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
index e42a7a3c0..ff5c10220 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
@@ -25,19 +25,18 @@ public class MonolithicShard implements Shard {
     /**
      * Locations.  For the monolithic shard, should be a list of all available contigs in the reference.
      */
-    private final List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
+    private final List<GenomeLoc> locs;
 
     /**
      * Creates a new monolithic shard of the given type.
      * @param shardType Type of the shard.  Must be either read or locus; cannot be intervalic.
-     * @param sequenceDictionary the sequence dictionary from which to derive contig info. 
+     * @param locs Intervals that this monolithic shard should process. 
      */
-    public MonolithicShard(ShardType shardType, SAMSequenceDictionary sequenceDictionary) {
+    public MonolithicShard(ShardType shardType, List<GenomeLoc> locs) {
         if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
             throw new StingException("Invalid shard type for monolithic shard: " + shardType);
         this.shardType = shardType;
-        for(SAMSequenceRecord sequenceRecord: sequenceDictionary.getSequences())
-            locs.add(GenomeLocParser.createGenomeLoc(sequenceRecord.getSequenceName(),1,sequenceRecord.getSequenceLength()));
+        this.locs = locs;
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
index 022213d37..c8c23dc49 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShardStrategy.java
@@ -5,6 +5,7 @@ import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Iterator;
 import java.util.NoSuchElementException;
+import java.util.List;
 
 import net.sf.samtools.SAMSequenceDictionary;
 
@@ -24,8 +25,8 @@ public class MonolithicShardStrategy implements ShardStrategy {
      * Create a new shard strategy for shards of the given type.
      * @param shardType The shard type.
      */
-    public MonolithicShardStrategy(final Shard.ShardType shardType, final SAMSequenceDictionary sequenceDictionary) {
-        shard = new MonolithicShard(shardType,sequenceDictionary);
+    public MonolithicShardStrategy(final Shard.ShardType shardType, final List<GenomeLoc> region) {
+        shard = new MonolithicShard(shardType,region);
     }
 
     /**