Small fixes for TRGT

[fellen31]

This PR adds | fixes:

• Allows TRID to not always have to have underscores (if repeat files comes from PacBio, and not STRchive)
• Allows for repeats that could not be genotyped. However, considering Flag coverage dropouts induced by repeat expansions in long-read data scout#4597, maybe these should get a STR_STATUS=no_call or similar?

How to prepare for test:

• ssh to ...
• Install on stage:
  bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]

How to test:

Expected outcome:

• [ ]

Review:

• Code approved by
• Tests executed by
• "Merge and deploy" approved by

This version is a:

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[dnil]

Thank you kindly! Sorry for the state of the onion; we haven't had a contribution here in a while. Cool, we can try to clean up a bit in time to make it easier to piece in new stuff!

[dnil]

If you like (its only two repetitions so far) a function like

def get_repeat_id(variant_info):

would be welcome, now that its a little bit more code. Besides it lowers apparent complexity with the less C-like and PEPpy.

if this:
    do this thing
    return this_thing
if that:
   do that thing
    return that_thing

[fellen31]

Absolutely!

[dnil]

Ah, I hadn't seen that one? Is that from TRGT or sth from STRdust? Do they mean completely missing from motifs, or is it a shorthand for as-reference? ExHu was kind enough to calculate and pass the reference size given the current locus definitions, but I guess for TRGT we would perhaps pass it from the repeat definition file.
We should check what the callers intended here I think!

[fellen31]

This is for TRGT. Probably when the repeat could not be called. Some examples:

chr16   17470908        .       GCCGCCGCCGCCGCCC        .       0       .       TRID=XYLT1;END=17470923;MOTIFS=GCC;STRUC=(GCC)n        GT:AL:ALLR:SD:MC:MS:AP:AM       .:.:.:.:.:.:.:.
chr16   24613440        .       TTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTATTTTAT    .       0       .       TRID=TNRC6A;END=24613530;MOTIFS=TTTTA,TTTCA;STRUC=(TTTTA)n(TTTCA)n(TTTTA)n      GT:AL:ALLR:SD:MC:MS:AP:AM      .:.:.:.:.:.:.:.
chr16   66490399        .       TAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAAAATAATAAAATAAAAA   .       0              .       TRID=BEAN1;END=66490467;MOTIFS=TGGAA,TAAAA;STRUC=(TGGAA)n(TAAAA)n       GT:AL:ALLR:SD:MC:MS:AP:AM              .:.:.:.:.:.:.:.

[dnil]

Ahoy! Yes, could be missing or reality saying hi with some unexpected alleles. I guess we also have to treat it as no-call rather than reference. It's unfortunate that TRGT does seem to set QUAL==0 and no FILTER=='.' for everything. For ExHu we did set the size to 0 for . so I guess we might as well here!

[fellen31]

I run a test-dataset with reads that only covers a few of the pathogenic repeats.

[fellen31]

I have made some updates the code @dnil, let me know what you think.

[dnil]

Thank you!

[dnil]

💯

[dnil]

👍

[fellen31]

Let me know if it's ok to merge.

Would be great if we could get a bioconda update as well, then I could add Stranger to Nallo (with TRGT for now).

[dnil]

I think this is good to go, but I noticed we have no Changelog-missing warning automation! 😁
Perhaps add a sentence to the unreleased section [x.x.x] here, then merge when you are done, and I can make a new release and update on PyPi. I will have to investigate how that works on bioconda: not sure if they will immediately update as well, or if we have to trigger it.