BREAKING CHANGE: v0.16 -> CBQ input/output implementation - #95
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alejandrogzi wants to merge 2 commits into
Open
BREAKING CHANGE: v0.16 -> CBQ input/output implementation#95alejandrogzi wants to merge 2 commits into
alejandrogzi wants to merge 2 commits into
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This PR includes the necessary implemenation for
deacon filterto accept CBQ (BINSEQ) input, detected automatically, and writes CBQ when the output path ends in.cbq. Benchmark output is consistent between any format combination.Main change against #31 is only CBQ support, dropping VBQ/BQ.
Benchmark: FASTQ vs CBQ, deacon filter 0.16.0
Input: 500k real viral reads (~4 kb each, 1.9 GB) from rsviruses17900 (Zenodo), filtered against an index built from the 17,900 virus contigs (rsviruses17900.fa.gz); keep-all thresholds (-a 1 -r 0), -t 8, 16-core box; hyperfine min/median of 3 + one /usr/bin/time -v pass for peak RSS.
Findings
*Paired reads were derived by half-splitting real reads.