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@jblachly jblachly commented Aug 9, 2016

Resolve issue #83 (Inclusion of literal TAB characters leads to violation of SAM spec)

@lh3 lh3 merged commit 1eee77a into lh3:master Jul 30, 2017
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:

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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