Hayden Metsky

Account for Illumina's read segment quality control indicator

1

Apparently Illumina uses the Q=2 quality score as a "Read Segment Quality Control Indicator". I can't find any recent mentions of this on Illumina's website. One document from 2011 describes...

Report read depth in VCF file for samples that do not have alternate alleles at a position

6

With #356, the VCF file created by `intrahost.py`'s `merge_to_vcf` reports read depth, at a given position, only for samples that contain alternate alleles at that position. If a sample has...

Enhance usability for large, diverse input

1

This PR aims to make CATCH more accessible to users via a single command and/or in case users overlook options that specifically enhance its runtime and memory usage. Specific goals...

This could wait until we accumulate a larger list of sticking points for users.