From 206df6fb193dee1051da0543fb17ad67d3149fac Mon Sep 17 00:00:00 2001 From: Daniel Date: Mon, 24 Feb 2020 13:57:43 -0500 Subject: [PATCH 1/2] Made File Executable By Adding Python3 Shebang --- celltics/tools/vargroup.py | 1 + 1 file changed, 1 insertion(+) diff --git a/celltics/tools/vargroup.py b/celltics/tools/vargroup.py index f1c83db..2d779e3 100755 --- a/celltics/tools/vargroup.py +++ b/celltics/tools/vargroup.py @@ -1,3 +1,4 @@ +#!/usr/bin/env python3 """ (c) MGH Center for Integrated Diagnostics From 30cdd66844c13382548e8931410b2b2b33a2734d Mon Sep 17 00:00:00 2001 From: Guru Date: Tue, 12 May 2020 14:33:13 -0400 Subject: [PATCH 2/2] Use ref_seq if specified irrespective of bam_file --- celltics/tools/vargroup.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/celltics/tools/vargroup.py b/celltics/tools/vargroup.py index 2d779e3..17a859e 100755 --- a/celltics/tools/vargroup.py +++ b/celltics/tools/vargroup.py @@ -587,9 +587,8 @@ def bam_and_merge_multiprocess(bam_file, vars_to_group, fq_threshold, min_reads, debug=False): """ Multiprocess inspect bam and merge step together """ fdict = None - if bam_file is not None: - if ref_seq is not None: - print('Opening reference sequence: {}'.format(ref_seq)) + if ref_seq is not None: + print('Opening reference sequence: {}'.format(ref_seq)) fdict = get_ref_seq_dict(ref_seq) start = time.time() var_chunks, chrom_pos = dict_chunks(vars_to_group, nthreads)