# HG changeset patch
# User jeremie
# Date 1404724371 14400
# Node ID 844ad5ce74cc730021c927f5fa98d7f90a8e089f
# Parent  de8a643a41e30395892ddcdf8b7985f8586c5bc3
Uploaded

diff -r de8a643a41e3 -r 844ad5ce74cc pindel.py
--- 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')