spVCF
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Sparse Project VCF: evolution of VCF to encode population genotype matrices efficiently
Since the NewEncoder & NewDecoder factory functions return a Transcoder object, this class needs to have a virtual destructor in order for the concrete object to be deleted properly and...
To help with approximate reconstruction of genotype likelihoods from binned DP (when downstream tools strictly require them to be present even in non-variant cells): 1. during encoding, calculate regression coefficients...
This would facilitate zero-transcoding htsget on `spvcf.gz`. Would need to use htslib BGZF primitives directly inside `spvcf` instead of piping into `bgzip`. Fallback idea: add a flag to the decoder...
1. Current logic extracts records with `POS >= qlo` (query low) but omits records with `POS < qlo && END >= qlo.` 2. More thorough testing would be nice. 3....
like `bcftools view -S` but take advantage of the "horizontal" run-encoding to do this more efficiently.
The middle-out checkpoint procedure can be skipped if we’re ok with sticking ./. in all non-variant cells