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biod / sambamba

Tools for working with SAM/BAM data
http://thebird.nl/blog/D_Dragon.html
GNU General Public License v2.0
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Not recognising bcftools version >=1.5 #350

Closed nathanhaigh closed 6 years ago

nathanhaigh commented 6 years ago

Since BCFtools 1.4.1 releases have been using a 2 digits for their versions (i.e. 1.5, 1.6, 1.7 and 1.8). As such, the code in Sambamba nolonger recognises the version string generated by BCFtools.

Unless Sambamba doesn't support BCFtools > 1.4.1 I think the offending line is: https://github.com/biod/sambamba/blob/cbae92752472d89a53e407cb198e4485d8fe8a4b/sambamba/pileup.d#L109

I would suggest a less constrained regex and perhaps following the same path as the version detection for SAMtools: https://github.com/biod/sambamba/blob/cbae92752472d89a53e407cb198e4485d8fe8a4b/sambamba/pileup.d#L90

nathanhaigh commented 6 years ago

This affects Sambamba v >0.6.5.

Commit https://github.com/biod/sambamba/commit/2d02baf055029ea3214f5d4fbef606b44e877fdd actually changed the version detection from the "samtools-like" version detection. Perhaps a better way is to just may the "patch" number optional in the regex.

A minimal change might

pjotrp commented 6 years ago

Good find. Will fix.