`handle_header` mangles alt contigs

brentp / bwa-meth

fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome

https://arxiv.org/abs/1401.1129

MIT License

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`handle_header` mangles alt contigs #79

Closed jdidion closed 2 years ago

jdidion commented 2 years ago

When using a reference with alt contigs, contigs with names of the form "HLA-A01:01:01:01" are truncated to "HLA-A01", which produces duplicate contig names in the output. If bwa-meth is not designed to work with alt contigs, please state this explicitly in the readme, otherwise this issue needs to be addressed. Thanks.

jdidion commented 2 years ago

My guess is that this is unintentional and can be fixed by adding maxsplit=1. I'll submit a PR.

brentp commented 2 years ago

closed by #80