Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@986 348d0f76-0448-11de-a6fe-93d51630548a

doc/ReadQualityRecalibrator/README

@@ -97,6 +97,17 @@ Known Issues
   graphs.  If running on a machine via ssh, be certain
   to enable X tunnelling.
 
+Troubleshooting
+---------------
+- The memory requirements of the recalibrator will 
+  vary based on the type of JVM running the application 
+  and the number of read groups in the input bam file.  
+  If the application reports 'java.lang.OutOfMemoryError:
+  Java heap space', increase the max heap size provided
+  to the JVM by adding ' -Xmx????m' to the jvm_args
+  variable in RecalQual.py, where '????' is the maximum
+  available memory on the processing computer.
+
 Support
 -------
 For support, please email gsadevelopers@broad.mit.edu.

python/RecalQual.py

@@ -6,7 +6,7 @@ java_exe='/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/bin/java'
 R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"
 
 # Any special site-specific arguments to pass the JVM.
-jvm_args='-ea -Xmx4096m'
+jvm_args='-ea'
 
 # Which platforms should the calibration tool be run over?
 platforms=['illumina']