Parse_locus() over multiple regions using GRCh38

[tpoterba]

In 0.2.15 or later, doing the following:

intervals = [hl.parse_locus(x, reference_genome='GRCh38') for x in ['4:144585304', '15:78575140']]
mt_hits = mt.filter_rows(hl.literal(intervals).contains(mt.locus))

will have the same performance as filter_intervals, but is much easier to use. See here:

New optimizer pass that extracts point queries and interval filters

hl.filter_intervals is one of the best ways to speed up pipelines that only need to look at a small fraction of your data, but the method is quite a pain to use compared to simpler methods like filter_rows. As of 0.2.15, Hail includes an optimizer pass that tries to rewrite filter / filter_rows method calls as filter_intervals when possible. This can make pipelines orders of magnitude faster, since it reduces the amount of data read from disk – and data you don’t read can’t slow you down! You’l…