Forbid literal TAB control characters in @RG line #84
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nsoranzo
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Nov 3, 2017
When using bwameth with bwa >=0.7.16 and not specifying `--read-group`, I'm getting the error already reported in brentp#44 (comment) i.e.: ``` [E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \t Traceback (most recent call last): File "/path/bin/bwa-meth-0.10/bwameth.py", line 601, in <module> main(sys.argv[1:]) File "/path/bin/bwa-meth-0.10/bwameth.py", line 586, in main set_as_failed=args.set_as_failed) File "/path/bwa-meth-0.10/bwameth.py", line 259, in bwa_mem as_bam(cmd, fa, prefix, calmd, set_as_failed) File "/path/bin/bwa-meth-0.10/bwameth.py", line 293, in as_bam raise Exception("bad or empty fastqs") Exception: bad or empty ``` This is due to the following change in bwa: xref. lh3/bwa#84
nsoranzo
added a commit
to nsoranzo/bwa-meth
that referenced
this pull request
Nov 3, 2017
When using bwameth with bwa >=0.7.16 and not specifying `--read-group`, I'm getting the error already reported in brentp#44 (comment) i.e.: ``` [E::bwa_set_rg] the read group line contained literal <tab> characters -- replace with escaped tabs: \t Traceback (most recent call last): File "/path/bin/bwa-meth-0.10/bwameth.py", line 601, in <module> main(sys.argv[1:]) File "/path/bin/bwa-meth-0.10/bwameth.py", line 586, in main set_as_failed=args.set_as_failed) File "/path/bwa-meth-0.10/bwameth.py", line 259, in bwa_mem as_bam(cmd, fa, prefix, calmd, set_as_failed) File "/path/bin/bwa-meth-0.10/bwameth.py", line 293, in as_bam raise Exception("bad or empty fastqs") Exception: bad or empty ``` This is due to the following change in bwa: lh3/bwa#84
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Resolve issue #83 (Inclusion of literal TAB characters leads to violation of SAM spec)