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CSB5 / lofreq

LoFreq Star: Sensitive variant calling from sequencing data
http://csb5.github.io/lofreq/
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Bcftools pparallel #109

Closed rdmorin closed 3 years ago

rdmorin commented 3 years ago

This pull request addresses a major issue that has been affecting us when we run Lofreq on whole genome data in somatic mode. Non-ACTGN characters in the reference (e.g. IUPAC ambiguity codes such as W, R, Y) cause strange behaviour and lead to malformed/garbled lines in the VCF somewhat consistently (see #106). The change to plp.c forces these positions to be ignored as it does for Ns in the reference. We have also changed merging to rely on bcftools in an earlier attempt to address this issue (see #108). That change may not be necessary at this point with the current patch to plp.c

I'm interested in having at least the plp.c change added to future releases of lofreq so conda users can benefit from this improvement.

andreas-wilm commented 3 years ago

Thank you so much!

Kdreval commented 3 years ago

Hi Andreas! We would greatly appreciate it this update will be considered for the next release of the conda version. Thank you in advance!

andreas-wilm commented 3 years ago

Absolutely. It's merged already and will be part of v2.1.6

Kdreval commented 3 years ago

Hi Andreas! There are updated files at Conda, but they seem to be without version bump and refer to v2.1.5. I could not find documentation what has been recently changed, but it seems that update from this PR hasn't been rolled out yet? Just want to remind about it, as it seems v2.1.6 is coming!

andreas-wilm commented 3 years ago

Hi Konstantin,

2.1.5 was released last year already (see Changelog https://github.com/CSB5/lofreq/blob/master/Changelog). Are you saying it was just included in Conda? Sorry, I'm not following this closely. 2.1.6 should come soon. But since I'm maintaining this as a hobby, things take a lot longer than I'd hoped.

Best, Andreas

On Fri, 16 Apr 2021 at 06:06, Kostiantyn Dreval @.***> wrote:

Hi Andreas! There are updated files at Conda, but they seem to be without version bump and refer to v2.1.5. I could not find documentation what has been recently changed, but it seems that update from this PR hasn't been rolled out yet? Just want to remind about it, as it seems v2.1.6 is coming!

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