Changing preloaded index to only "preload" reference sequences on demand.

Results in drastic lowering of startup cost when multiple BAM files are 
merged.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/BAMFileStat.java

@@ -80,6 +80,7 @@ public class BAMFileStat extends CommandLineProgram {
         }
 
         public void inspect(PrintStream outputStream, Integer startPosition, Integer stopPosition) {
+            /*
             outputStream.printf("Number of reference sequences: %d%n", this.referenceToBins.size());
             for(int referenceSequence: referenceToBins.keySet()) {
                 Bin[] bins = referenceToBins.get(referenceSequence);
@@ -97,6 +98,7 @@ public class BAMFileStat extends CommandLineProgram {
                     outputStream.printf("%d,",indexEntry);
                 outputStream.printf("%n");
             }
+            */
         }
     }
 }

settings/repository/edu.mit.broad/picard-private-parts-1333-sharding-3.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-2" status="integration" publication="20100319183800" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1333-sharding-3" status="integration" publication="20100323163000" />
 </ivy-module>

settings/repository/net.sf/picard-1.16.363-sharding.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.16.362-sharding" status="release" />
+    <info organisation="net.sf" module="picard" revision="1.16.363-sharding" status="release" />
 </ivy-module>

settings/repository/net.sf/sam-1.16.363-sharding.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.16.362-sharding" status="release" />
+    <info organisation="net.sf" module="sam" revision="1.16.363-sharding" status="release" />
 </ivy-module>