jamescasbon/PyVCF — pull request #40 by libor-m (2012-04-19 10:14:56+00:00)
Title: improvments to vcf_filter

I like the idea of vcf filtering framework, so I tried to use that for my project. To be able to use that fluently, i've added few changes.

#### Filter classes can be contained in local file
The file is given on the command line, so not all the possible arguments are known the first time command line is parsed. So it was necessary to slightly change the command syntax to

vcf_filter.py --optionals input filter1 [--filter1-optionals]
[filter2 [--filter2-optionals]]

This way the arguments can be parsed filter by filter and checked for correctness.
#### Output 'PASS' in filter field only if filtered data are not dropped
#### Small change to ``add_filter()`` to remove the '.' when adding first filter