Mercurial > repos > blankenberg > naive_variant_caller
comparison tools/naive_variant_caller.py @ 8:d5f866df45ae
Uploaded
| author | blankenberg |
|---|---|
| date | Thu, 29 Jan 2015 15:02:01 -0500 |
| parents | 8398666758e3 |
| children | ac0235d2d459 |
comparison
equal
deleted
inserted
replaced
| 7:3c3ef33b9d56 | 8:d5f866df45ae |
|---|---|
| 16 parser.add_option( '-s', '--use_strand', dest='use_strand', action='store_true', default = False, help='Report counts by strand' ) | 16 parser.add_option( '-s', '--use_strand', dest='use_strand', action='store_true', default = False, help='Report counts by strand' ) |
| 17 parser.add_option( '-p', '--ploidy', dest='ploidy', action='store', type="int", default=2, help='Ploidy. Default=2.' ) | 17 parser.add_option( '-p', '--ploidy', dest='ploidy', action='store', type="int", default=2, help='Ploidy. Default=2.' ) |
| 18 parser.add_option( '-d', '--min_support_depth', dest='min_support_depth', action='store', type="int", default=0, help='Minimum number of reads needed to consider a REF/ALT. Default=0.' ) | 18 parser.add_option( '-d', '--min_support_depth', dest='min_support_depth', action='store', type="int", default=0, help='Minimum number of reads needed to consider a REF/ALT. Default=0.' ) |
| 19 parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' ) | 19 parser.add_option( '-q', '--min_base_quality', dest='min_base_quality', action='store', type="int", default=None, help='Minimum base quality.' ) |
| 20 parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' ) | 20 parser.add_option( '-m', '--min_mapping_quality', dest='min_mapping_quality', action='store', type="int", default=None, help='Minimum mapping.' ) |
| 21 parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default='uint64', help='dtype to use for coverage array' ) | 21 parser.add_option( '-t', '--coverage_dtype', dest='coverage_dtype', action='store', type="string", default=None, help='dtype to use for coverage array' ) |
| 22 parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' ) | 22 parser.add_option( '--allow_out_of_bounds_positions', dest='allow_out_of_bounds_positions', action='store_true', default = False, help='Allows out of bounds positions to not throw fatal errors' ) |
| 23 parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' ) | 23 parser.add_option( '--safe', dest='safe', action='store_true', default = False, help='Perform checks to prevent certain errors. Is slower.' ) |
| 24 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' ) | 24 parser.add_option( '--region', dest='region', action='append', type="string", default=[], help='region' ) |
| 25 (options, args) = parser.parse_args() | 25 (options, args) = parser.parse_args() |
| 26 | 26 |