added max_sr_support and max_pe_support options to filter-merge

arcsv/filter_output.py

@@ -150,10 +150,16 @@ def apply_filters(opts, records, header):
         supporting_splits = [int(x) for x in sv[col_lookup['sr_support']].split(',')]
         if min(supporting_splits) < opts['min_sr_support']:
             continue
+        if opts['max_sr_support'] is not None and \
+           max(supporting_splits) > opts['max_sr_support']:
+            continue
         # discordant paired-end read support
         supporting_pe = [int(x) for x in sv[col_lookup['pe_support']].split(',')]
         if min(supporting_pe) < opts['min_pe_support']:
             continue
+        if opts['max_pe_support'] is not None and \
+           max(supporting_pe) > opts['max_pe_support']:
+            continue
         # allele fraction
         af = float(sv[col_lookup['af']])
         if af < opts['min_allele_fraction'] or af > opts['max_allele_fraction']:

bin/arcsv

@@ -117,9 +117,11 @@ def add_filter_parser(subparsers):
     parser_filter.add_argument('--min_sr_support', required=False, type=int, default=0,
                                help='minimum supporting split reads '
                                     '(required at each breakpoint in case num_sv > 1)')
+    parser_filter.add_argument('--max_sr_support', required=False, type=int)
     parser_filter.add_argument('--min_pe_support', required=False, type=int, default=0,
                                help='minimum supporting discordant read pair cluster size '
                                     '(required at each breakpoint in case num_sv > 1)')
+    parser_filter.add_argument('--max_pe_support', required=False, type=int)
     parser_filter.add_argument('--min_allele_fraction', required=False, type=float, default=0,
                                help='minimum predicted allele fraction of alternate alleles')
     parser_filter.add_argument('--max_allele_fraction', required=False, type=float, default=1,