Mercurial > repos > jeremie > pindel_test
changeset 9:844ad5ce74cc draft
Uploaded
| author | jeremie |
|---|---|
| date | Mon, 07 Jul 2014 05:12:51 -0400 |
| parents | de8a643a41e3 |
| children | accf671c1f3d |
| files | pindel.py |
| diffstat | 1 files changed, 8 insertions(+), 8 deletions(-) [+] |
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--- a/pindel.py Mon Jul 07 05:05:50 2014 -0400 +++ b/pindel.py Mon Jul 07 05:12:51 2014 -0400 @@ -18,19 +18,19 @@ parser.add_argument('--report_inversions', dest='report_inversions', action='store_true', default=False) parser.add_argument('--report_breakpoints', dest='report_breakpoints', action='store_true', default=False) -parser.add_argument('--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default='0.02') +parser.add_argument('-u', '--maximum_allowed_mismatch_rate', dest='maximum_allowed_mismatch_rate', type=float, default='0.02') parser.add_argument('--report_close_mapped_reads', dest='report_close_mapped_reads', action='store_true', default=False) parser.add_argument('--report_only_close_mapped_reads', dest='report_only_close_mapped_reads', action='store_true', default=False) parser.add_argument('--report_interchromosomal_events', dest='report_interchromosomal_events', action='store_true', default=False) parser.add_argument('--IndelCorrection', dest='IndelCorrection', action='store_true', default=False) parser.add_argument('--NormalSamples', dest='NormalSamples', action='store_true', default=False) -parser.add_argument('--additional_mismatch', dest='additional_mismatch', type=int, default='1') -parser.add_argument('--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default='3') -parser.add_argument('--min_inversion_size', dest='min_inversion_size', type=int, default='50') -parser.add_argument('--min_num_matched_bases', dest='min_num_matched_bases', type=int, default='30') -parser.add_argument('--balance_cutoff', dest='balance_cutoff', type=int, default='0') -parser.add_argument('--anchor_quality', dest='anchor_quality', type=int, default='0') -parser.add_argument('--minimum_support_for_event', dest='minimum_support_for_event', type=int, default='3') +parser.add_argument('-a', '--additional_mismatch', dest='additional_mismatch', type=int, default='1') +parser.add_argument('-m', '--min_perfect_match_around_BP', dest='min_perfect_match_around_BP', type=int, default='3') +parser.add_argument('-v', '--min_inversion_size', dest='min_inversion_size', type=int, default='50') +parser.add_argument('-d', '--min_num_matched_bases', dest='min_num_matched_bases', type=int, default='30') +parser.add_argument('-B', '--balance_cutoff', dest='balance_cutoff', type=int, default='0') +parser.add_argument('-A', '--anchor_quality', dest='anchor_quality', type=int, default='0') +parser.add_argument('-M', '--minimum_support_for_event', dest='minimum_support_for_event', type=int, default='3') parser.add_argument('--detect_DD', dest='detect_DD', action='store_true', default=False) parser.add_argument('--MAX_DD_BREAKPOINT_DISTANCE', dest='MAX_DD_BREAKPOINT_DISTANCE', type=int, default='350') parser.add_argument('--MAX_DISTANCE_CLUSTER_READS', dest='MAX_DISTANCE_CLUSTER_READS', type=int, default='100')