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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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Edit suggested: Escape tab characters to resolve BWA error #18

Closed pvishwa2 closed 5 years ago

pvishwa2 commented 5 years ago

https://github.com/CPTR-ReSeqTB/UVP/blob/55fd74cd5436d36cb6e7ec64c5368f1671af1529/scripts/UVP.py#L251

That line seems to be giving me some issue in the BWA step. Not sure if I'm the only one. MY command line interprets the statement with tab characters when calling, and that throws up the " [E::bwa_set_rg] the read group line contained literal characters -- replace with escaped tabs: \t" error.

I fixed my version by doubling up the escape characters, so the line is this instead: "@RG\\tID:" + self.name + "\\tSM:" + self.name + "\\tPL:ILLUMINA",

alantsangmb commented 5 years ago

I encounter this problem too, and your method helps by adding the backslash escape character. Thanks.