--keep-zeros: Don't truncate outputs by omitting locations with 0 depth
skip-merging-intervals: If a BED or VCF/BCF file is provided, don't merge the intervals found within, this will produce duplicate entries. This is useful in some niche cases when looking at fixed windows around sites that are then fed into matrices.
Adds:
--keep-zeros
: Don't truncate outputs by omitting locations with 0 depthskip-merging-intervals
: If a BED or VCF/BCF file is provided, don't merge the intervals found within, this will produce duplicate entries. This is useful in some niche cases when looking at fixed windows around sites that are then fed into matrices.gzp
instead of noodles for bgzf support for reading and writing. Now supports multi-threaded writer