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comparison shear_wrapper.py @ 8:8fac6c7d32fd

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Copy reference fasta for shear sv to avoid GATK issue with symlinks
author Jim Johnson <jj@umn.edu>
date Tue, 22 Oct 2013 09:44:32 -0500
parents 0158f7356ffd
children
comparison
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7:8180f6b0249b 8:8fac6c7d32fd
45 args = [ 'java','-jar' ] 45 args = [ 'java','-jar' ]
46 args.append( options.jar_path ) 46 args.append( options.jar_path )
47 args.append( command ) 47 args.append( command )
48 # Check required params for command 48 # Check required params for command
49 buffsize = 1048576 49 buffsize = 1048576
50 copy_ref = False 50 copy_ref = True
51 prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref' 51 prefix = options.prefix if options.prefix and len(options.prefix) > 0 else 'ref'
52 if command in ['sv']: 52 if command in ['sv']:
53 args.append( '-p' ) 53 args.append( '-p' )
54 args.append( prefix ) 54 args.append( prefix )
55 if options.sv_only: 55 if options.sv_only:
56 args.append('--sv-only') 56 args.append('--sv-only')
57 if options.region: 57 if options.region:
58 args.append('-r') 58 args.append('-r')
59 args.append(options.region) 59 args.append(options.region)
60 copy_ref = True # GATK has issue with symlinks for .fa and .fai
60 if options.svidx_dir and command in ['sv']: 61 if options.svidx_dir and command in ['sv']:
61 if not os.path.isdir(options.svidx_dir): 62 if not os.path.isdir(options.svidx_dir):
62 os.makedirs(options.svidx_dir) 63 os.makedirs(options.svidx_dir)
63 ref_prefix = os.path.join(options.svidx_dir,prefix) 64 ref_prefix = os.path.join(options.svidx_dir,prefix)
64 copy_ref = True 65 copy_ref = True