minor updates for speed improvements

czbiohub-sf / MIDAS

Metagenomic Intra-Species Diversity Analysis (MIDAS)

MIT License

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minor updates for speed improvements #57

Closed zhaoc1 closed 3 years ago

zhaoc1 commented 3 years ago

1) Temp file structure: {species_id} {chunk_id} {within_chunk_contig_id} 2) Two pass of parsing BAM file for the run snps flow, despise paired-only or not.