Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5549 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java

@@ -580,4 +580,8 @@ public class GATKBAMIndex implements BAMIndex, BrowseableBAMIndex {
     protected long position() {
         return mFileBuffer.position();
     }
+
+    @Override
+    public void close() {
+    }
 }

java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java

@@ -752,6 +752,7 @@ public class SAMDataSource {
             for(SAMReaderID readerID: readerIDs) {
                 SAMFileReader reader = new SAMFileReader(readerID.samFile);
                 reader.enableFileSource(true);
+                reader.enableIndexMemoryMapping(false);
                 if(!enableLowMemorySharding)
                     reader.enableIndexCaching(true);
                 reader.setValidationStringency(validationStringency);

settings/repository/edu.mit.broad/picard-private-parts-1816.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1702" status="integration" publication="20110102175300" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1816" status="integration" publication="20110102175300" />
 </ivy-module>

settings/repository/net.sf/picard-1.37.686.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.37.686" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.42.773.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.42.773" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.37.686.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.37.686" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.42.773.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.42.773" status="release" />
+</ivy-module>