Mercurial > repos > jjohnson > shear
comparison shear_wrapper.py @ 8:8fac6c7d32fd
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 |
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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 |