File: filter.feature

package info (click to toggle)
bio-vcf 0.9.5-4
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid
  • size: 1,208 kB
  • sloc: ruby: 2,812; sh: 74; lisp: 48; makefile: 4
file content (12 lines) | stat: -rw-r--r-- 610 bytes parent folder | download | duplicates (3) 
1
2
3
4
5
6
7
8
9
10
11
12
 
@filter
Feature: Adding filters

  bio-vcf can add soft filters. Rather than removing failing items we can
  inject filter state into the FILTER field. To add state such as PASS or
  LowDepth simply use a filter and the --set-filter switch. If a filter already
  has state the new one is appended with a semi-colon.
  
  Scenario: Test the info filter using dp and threads
    Given I have input file(s) named "test/data/input/somaticsniper.vcf"
    When I execute "./bin/bio-vcf --add-filter PASS --filter 'r.normal.dp>5 and r.tumor.dp>7'"
    Then I expect the named output to match the named output "pass1"