new sub-command gemini index

[brentp]

usage will be:

gemini index $name `$expression` $db

where expression is a genotype filter expression that returns True or False. And $name is the name of the new column. e.g.

gemini index proband_het_depth gt_types.sample_1 == HET and (gt_depths).(*).(>=10).(all)`

This will create a new, indexed column proband_het that users can then add to their queries to increase reliance on the database's indexing (which is fast) rather than on the internal machinery in gemini (which isn't fast).

Use of that column will look like this:

gemini de_novo --filter "max_aaf_all < 0.005 AND proband_het_depth = 1" --columns "chrom, start, end..." $db

[arq5x]

+10