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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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match behavior of extract_sv_reads and samblaster #272

Closed brentp closed 5 years ago

brentp commented 5 years ago

this also uses @ernfrid 's method of dropping sequence and qualities from the split and disc bams. This makes the files about half the size and the memory (of uncompressed bam1_t) savings is dramatic.

It also fixes multi-threading of CRAM and uses minimal (level 1) gzip compression.

cc @ryanlayer @ernfrid