nhoffman / barcodecop Goto Github PK

If we allow barcodecop to handle empty files gracefully, we could avoid the need to pre-screen inputs.

cc @crosenth

Motivated by https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3217-x

We observed rates of cross-talk averaging 0.24 % when multiplexing 14 different samples with unique i5 and i7 index sequences. This cross-talk rate corresponded to 254,632 misassigned reads on a single lane of the Illumina HiSeq 2500. Notably, all types of misassignment occur at similar rates: incorrect i5, incorrect i7, and incorrect sequence reads. We demonstrate that misassignments can be nearly eliminated by quality filtering of index reads while preserving about 90 % of the original sequences.

add option --match-filter to make exact match enforcement optional. Raise an error (or warning?) if neither --qual-filter nor --match-filter is provided. This should be tagged as v0.4 since it represents an API change.

This change to the fastalite package introduces an optional argument to fastalite.fastqlite to 'allow_empty' sequence and quality values, for instance as may occur in an adaptor trimmed fastq.

I suggest adding an option to output --show-counts output to a CSV file.