From 0ead5ed0bf9347e9afdc4ee9f056bdb3414779c3 Mon Sep 17 00:00:00 2001 From: swingingsimian Date: Mon, 15 Aug 2016 10:25:02 +0100 Subject: [PATCH] Added functionality to pass through unkown command line arguments to bwa_mem extra_args --- bwameth.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/bwameth.py b/bwameth.py index c0deb23..ae956cb 100755 --- a/bwameth.py +++ b/bwameth.py @@ -597,11 +597,12 @@ def main(args=sys.argv[1:]): "multiple sets separated by commas, e.g. ... a_R1.fastq,b_R1.fastq" " a_R2.fastq,b_R2.fastq note that the order must be maintained.") - args = p.parse_args(args) + args, pass_through_args = p.parse_known_args(args) + # for the 2nd file. use G => A and bwa's support for streaming. conv_fqs_cmd = convert_fqs(args.fastqs) - bwa_mem(args.reference, conv_fqs_cmd, "", prefix=args.prefix, + bwa_mem(args.reference, conv_fqs_cmd, ' '.join(map(str, pass_through_args)), prefix=args.prefix, threads=args.threads, rg=args.read_group or rname(*args.fastqs), calmd=args.calmd, paired=len(args.fastqs) == 2,