Only truncate once before updating frequencies

This fixes a bug where we were only seeing the frequencies being updated for the last cohort in the list. This was a result of the placement of the truncate command. Previously, the truncation happened every loop iteration. Now, it happens before the loop starts.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Sort genes by effect impact in gene rank command

This also updates the test to be more general with regard to checking
that scores were added.

Signed-off-by: Don Naegely <naegelyd@gmail.com>
Merge pull request #243 from cbmi/issue-238

Only truncate once before updating frequencies
Merge pull request #244 from cbmi/issue-236

Sort genes by effect impact in gene rank command
Create test for allele frequency calculation

Signed-off-by: Ryan O'Hara <oharar@email.chop.edu>
Merge pull request #246 from ryanjohara/allele-freq-test

Create test for allele frequency calculation
Optimize the SolveBio ClinVar query to prevent slow variant resource requests

Remove the by-gene filter to narrow down the result sets and return only the first 10 results from the query.
Adds the total result count to the clinvar dictionary in the variant resource. Also fixes an issue with the genomic position filter.

Signed-off-by: David Caplan <dcaplan@gmail.com>