Mercurial > repos > jeremie > pindel_test

comparison pindel.py @ 9:844ad5ce74cc draft

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Uploaded
author jeremie
date Mon, 07 Jul 2014 05:12:51 -0400
parents de8a643a41e3
children accf671c1f3d
comparison
equal deleted inserted replaced
8:de8a643a41e3 9:844ad5ce74cc
16 parser.add_argument('--report_long_insertions', dest='report_long_insertions', action='store_true', default=False) 16 parser.add_argument('--report_long_insertions', dest='report_long_insertions', action='store_true', default=False)
17 parser.add_argument('--report_duplications', dest='report_duplications', action='store_true', default=False) 17 parser.add_argument('--report_duplications', dest='report_duplications', action='store_true', default=False)
18 parser.add_argument('--report_inversions', dest='report_inversions', action='store_true', default=False) 18 parser.add_argument('--report_inversions', dest='report_inversions', action='store_true', default=False)
19 parser.add_argument('--report_breakpoints', dest='report_breakpoints', action='store_true', default=False) 19 parser.add_argument('--report_breakpoints', dest='report_breakpoints', action='store_true', default=False)
20 20
21 parser.add_argument('--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default='0.02') 21 parser.add_argument('-u', '--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default='0.02')
22 parser.add_argument('--report_close_mapped_reads', dest='report_close_mapped_reads', action='store_true', default=False) 22 parser.add_argument('--report_close_mapped_reads', dest='report_close_mapped_reads', action='store_true', default=False)
23 parser.add_argument('--report_only_close_mapped_reads', dest='report_only_close_mapped_reads', action='store_true', default=False) 23 parser.add_argument('--report_only_close_mapped_reads', dest='report_only_close_mapped_reads', action='store_true', default=False)
24 parser.add_argument('--report_interchromosomal_events', dest='report_interchromosomal_events', action='store_true', default=False) 24 parser.add_argument('--report_interchromosomal_events', dest='report_interchromosomal_events', action='store_true', default=False)
25 parser.add_argument('--IndelCorrection', dest='IndelCorrection', action='store_true', default=False) 25 parser.add_argument('--IndelCorrection', dest='IndelCorrection', action='store_true', default=False)
26 parser.add_argument('--NormalSamples', dest='NormalSamples', action='store_true', default=False) 26 parser.add_argument('--NormalSamples', dest='NormalSamples', action='store_true', default=False)
27 parser.add_argument('--additional_mismatch', dest='additional_mismatch', type=int, default='1') 27 parser.add_argument('-a', '--additional_mismatch', dest='additional_mismatch', type=int, default='1')
28 parser.add_argument('--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default='3') 28 parser.add_argument('-m', '--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default='3')
29 parser.add_argument('--min_inversion_size', dest='min_inversion_size', type=int, default='50') 29 parser.add_argument('-v', '--min_inversion_size', dest='min_inversion_size', type=int, default='50')
30 parser.add_argument('--min_num_matched_bases', dest='min_num_matched_bases', type=int, default='30') 30 parser.add_argument('-d', '--min_num_matched_bases', dest='min_num_matched_bases', type=int, default='30')
31 parser.add_argument('--balance_cutoff', dest='balance_cutoff', type=int, default='0') 31 parser.add_argument('-B', '--balance_cutoff', dest='balance_cutoff', type=int, default='0')
32 parser.add_argument('--anchor_quality', dest='anchor_quality', type=int, default='0') 32 parser.add_argument('-A', '--anchor_quality', dest='anchor_quality', type=int, default='0')
33 parser.add_argument('--minimum_support_for_event', dest='minimum_support_for_event', type=int, default='3') 33 parser.add_argument('-M', '--minimum_support_for_event', dest='minimum_support_for_event', type=int, default='3')
34 parser.add_argument('--detect_DD', dest='detect_DD', action='store_true', default=False) 34 parser.add_argument('--detect_DD', dest='detect_DD', action='store_true', default=False)
35 parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE', dest='MAX_DD_BREAKPOINT_DISTANCE', type=int, default='350') 35 parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE', dest='MAX_DD_BREAKPOINT_DISTANCE', type=int, default='350')
36 parser.add_argument('--MAX_DISTANCE_CLUSTER_READS', dest='MAX_DISTANCE_CLUSTER_READS', type=int, default='100') 36 parser.add_argument('--MAX_DISTANCE_CLUSTER_READS', dest='MAX_DISTANCE_CLUSTER_READS', type=int, default='100')
37 parser.add_argument('--MIN_DD_CLUSTER_SIZE', dest='MIN_DD_CLUSTER_SIZE', type=int, default='3') 37 parser.add_argument('--MIN_DD_CLUSTER_SIZE', dest='MIN_DD_CLUSTER_SIZE', type=int, default='3')
38 parser.add_argument('--MIN_DD_BREAKPOINT_SUPPORT', dest='MIN_DD_BREAKPOINT_SUPPORT', type=int, default='3') 38 parser.add_argument('--MIN_DD_BREAKPOINT_SUPPORT', dest='MIN_DD_BREAKPOINT_SUPPORT', type=int, default='3')