consensus SNVs - lancet rerun needed

[jharenza]

What data file(s) does this issue pertain to?

SNV consensus

https://github.com/d3b-center/bixu-tracker/issues/2143

What release are you using?

v15

Put your question or report your issue here.

🐛

[Required] Which git repo contains the tools/workflows that you've found a bug in?

Somatic Workflow

[Required] Which tools/workflows need to be fixed?

https://github.com/kids-first/kf-somatic-workflow/blob/master/workflow/kfdrc-somatic-variant-workflow.cwl#L759-L770

[Required] Please describe the expected behavior, what the actual behavior is. If you have a suggestion, please add it!

In the task below we can see what is happening in a failing scenario:
https://cavatica.sbgenomics.com/u/kfdrc-harmonization/kf-reference-pipeline/tasks/4a0a0b24-fefe-4e84-ad67-06b1afb6abca/stats/

BEDops will fail with the following error:

2023-10-06T02:33:35.299416739Z Error: Could not find newline in intermediate buffer; check input [37883 | 3226 | 41109]
2023-10-06T02:33:35.299444466Z        Please check that your input contains Unix newlines (cat -A) or increase TOKENS_MAX_LENGTH in BEDOPS.Constants.hpp and recompile BEDOPS.

This error seems to be happening for Strelka2 inputs. My best guess is that there's some variant reported by strelka2 that is tripping up bedops.

A quick google search came up with the following: https://www.biostars.org/p/283321/. It appears there was an alteration made in our version for speedup purposes that causes this error to be thrown.

This error can be circumvented by changing to the megarow binary: switch-BEDOPS-binary-type --megarow. I have tested this locally and it works.

Assessment for this is that this affects mostly NON-CODING regions.

[jharenza]

This has been completed and will be in the next merge