# HG changeset patch
# User yufei-luo
# Date 1386683303 18000
# Node ID 22449c3a0b7fe6018701c8e131882e53bea486b5
# Parent  8409cff2d740ba0aa9b3c6f482e8bb3769f4f8c9
debug when use 'history' input fasta as genome reference

diff -r 8409cff2d740 -r 22449c3a0b7f bwa_0_7_5/bwa_0_7_5.py
--- a/bwa_0_7_5/bwa_0_7_5.py	Fri Nov 29 04:59:38 2013 -0500
+++ b/bwa_0_7_5/bwa_0_7_5.py	Tue Dec 10 08:48:23 2013 -0500
@@ -66,7 +66,7 @@
     parser.add_argument( '-p', '--interPairEnd', default=False, help='first query file consists of interleaved paired-end sequences' )
     parser.add_argument( '--rgid', help='Read group identifier' )
     parser.add_argument( '--rgsm', help='Sample' )
-    parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' )
+    parser.add_argument( '--rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT', 'PACBIO' ], help='Platform/technology used to produce the reads' )
     parser.add_argument( '--rglb', help='Library name' )
     parser.add_argument( '--rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' )
     parser.add_argument( '--rgcn', help='Sequencing center that produced the read' )
@@ -122,7 +122,8 @@
     tmp_index_dir = tempfile.mkdtemp()
     tmp_dir = tempfile.mkdtemp()
     # index if necessary
-    if args.fileSource == 'history' and not args.do_not_build_index:
+    # if args.fileSource == 'history' and not args.do_not_build_index:
+    if args.fileSource == 'history' :
         ref_file = tempfile.NamedTemporaryFile( dir=tmp_index_dir )
         ref_file_name = ref_file.name
         ref_file.close()