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Fix to use ref_seq if specified irrespective of bam_file #14

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Fix to use ref_seq if specified irrespective of bam_file #14

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206df6f
Made File Executable By Adding Python3 Shebang
Feb 24, 2020
30cdd66
Use ref_seq if specified irrespective of bam_file
May 12, 2020
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6 changes: 3 additions & 3 deletions celltics/tools/vargroup.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
#!/usr/bin/env python3
"""
(c) MGH Center for Integrated Diagnostics

Expand Down Expand Up @@ -586,9 +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)
Expand Down