From 04e51c8d1d7e9082d19537974d5da7f3ba2fd2ce Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 21 May 2009 22:26:19 +0000
Subject: [PATCH] Better version of MergeBAMBatch -- more options for creating
 the file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@787 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/MergeBAMBatch.py | 5 ++++-
 python/farm_commands.py | 6 ++++--
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/python/MergeBAMBatch.py b/python/MergeBAMBatch.py
index 5c643fe38..e950aae8d 100755
--- a/python/MergeBAMBatch.py
+++ b/python/MergeBAMBatch.py
@@ -22,6 +22,9 @@ if __name__ == "__main__":
     parser.add_option("-i", "--ignoreExistingFiles", dest="ignoreExistingFiles",
                         action='store_true', default=False,
                         help="Ignores already written files, if present")
+    parser.add_option("-m", "--mergeBin", dest="mergeBin",
+                        type="string", default=MERGE_BIN,
+                        help="Path to merge binary")
 
     (OPTIONS, args) = parser.parse_args()
     if len(args) != 1:
@@ -45,7 +48,7 @@ if __name__ == "__main__":
             sources = reduce( operator.__add__, map( glob.glob, s[1:] ), [] )
             
             if OPTIONS.ignoreExistingFiles or not os.path.exists(output_filename):
-                cmd = 'java -Xmx4096m -jar ' + MERGE_BIN + ' AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
+                cmd = 'java -Xmx4096m -jar ' + OPTIONS.mergeBin + ' MSD=true AS=true SO=coordinate O=' + output_filename + ' VALIDATION_STRINGENCY=SILENT ' + ' I=' + (' I='.join(sources))
                 print cmd
                 farm_commands.cmd(cmd, OPTIONS.farmQueue, output)
 
diff --git a/python/farm_commands.py b/python/farm_commands.py
index 7d33aaf46..e1d44f420 100644
--- a/python/farm_commands.py
+++ b/python/farm_commands.py
@@ -3,7 +3,7 @@
 import os
 #justPrintCommands = False
 
-def cmd(cmd_str, farm_queue=False, output_head=None, just_print_commands=False, outputFile = None):
+def cmd(cmd_str_from_user, farm_queue=False, output_head=None, just_print_commands=False, outputFile = None):
     # if farm_queue is non-False, submits to queue, other
 
     if farm_queue:
@@ -14,12 +14,14 @@ def cmd(cmd_str, farm_queue=False, output_head=None, just_print_commands=False,
         else:
             farm_stdout = None
             
-        cmd_str = "bsub -q "+farm_queue+" "+cmd_str 
+        cmd_str = "bsub -q "+farm_queue 
         if farm_stdout <> None:
             cmd_str += " -o " + farm_stdout
+        cmd_str += " "+cmd_str_from_user
         
         print ">>> Farming via "+cmd_str
     else:
+        cmd_str = cmd_str_from_user
         print ">>> Executing "+cmd_str
 
     if just_print_commands or (globals().has_key("justPrintCommands") and globals().justPrintCommands):