From fb3cc804dd3f3ef586ce3d3fab52f2c512ee4730 Mon Sep 17 00:00:00 2001
From: Dave Larson <dlarson@genome.wustl.edu>
Date: Thu, 17 Nov 2016 21:15:38 -0600
Subject: [PATCH] update genotype for new svtyper (v0.1.0)

---
 svtools/genotype.py | 25 +++++++++++--------------
 1 file changed, 11 insertions(+), 14 deletions(-)

diff --git a/svtools/genotype.py b/svtools/genotype.py
index bbf049b0..41747e0d 100644
--- a/svtools/genotype.py
+++ b/svtools/genotype.py
@@ -9,17 +9,15 @@ def __init__(self):
     @staticmethod
     def svtyper_option_lut():
         opts = { 
-                'bam' : '-B',
-                'split_bam' : '-S',
                 'input_vcf' : '-i',
                 'output_vcf' : '-o',
-                'splflank' : '-f',
-                'discflank' : '-F',
+                'bam' : '-B',
+                'lib_info' : '-l',
+                'min_aligned' : '-m',
+                'num_samp' : '-n',
                 'split_weight' : '--split_weight',
                 'disc_weight' : '--disc_weight',
-                'num_samp' : '-n',
-                'legacy' : '-M',
-                'debug' : '--debug',
+                'write_alignment' : '-w'
                 }
         return opts
 
@@ -27,17 +25,16 @@ def description():
     return 'compute genotype of structural variants based on breakpoint depth'
 
 def add_arguments_to_parser(parser):
-    parser.add_argument('-B', '--bam', type=str, required=True, help='BAM file(s), comma-separated if genotyping multiple BAMs')
-    parser.add_argument('-S', '--split_bam', type=str, required=False, help='split-read bam file for sample, comma-separated if genotyping multiple BAMs')
     parser.add_argument('-i', '--input_vcf', help='VCF input (default: stdin)')
     parser.add_argument('-o', '--output_vcf', help='output VCF to write (default: stdout)')
-    parser.add_argument('-f', '--splflank', type=int, required=False, default=20, help='min number of split read query bases flanking breakpoint on either side [20]')
-    parser.add_argument('-F', '--discflank', type=int, required=False, default=20, help='min number of discordant read query bases flanking breakpoint on either side. (should not exceed read length) [20]')
+    parser.add_argument('-B', '--bam', type=str, required=True, help='BAM or CRAM file(s), comma-separated if genotyping multiple BAMs')
+    parser.add_argument('-l', '--lib_info', type=str, required=False, help='create/read JSON file of library information')
+    parser.add_argument('-m', '--min_aligned', type=int, required=False, default=20, help='minimum number of aligned bases to consider read as evidence [20]')
+    parser.add_argument('-n', dest='num_samp', type=int, required=False, default=1000000, help='number of pairs to sample from BAM file for building insert size distribution [1000000]')
     parser.add_argument('--split_weight', type=float, required=False, default=1, help='weight for split reads [1]')
     parser.add_argument('--disc_weight', type=float, required=False, default=1, help='weight for discordant paired-end reads [1]')
-    parser.add_argument('-n', dest='num_samp', type=int, required=False, default=1000000, help='number of pairs to sample from BAM file for building insert size distribution [1000000]')
-    parser.add_argument('-M', action='store_true', dest='legacy', required=False, help='split reads are flagged as secondary, not supplementary. For compatibility with legacy BWA-MEM "-M" flag')
-    parser.add_argument('--debug', action='store_true', help='debugging verbosity')
+    parser.add_argument('-w', '--write_alignment', type=str, required=False, default=None, help='write relevant reads to BAM file')
+    parser.add_argument('--debug', action='store_true', help=argparse.SUPPRESS)
     parser.set_defaults(entry_point=run_from_args)
 
 def command_parser():