improvments to vcf_filter #40

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merged 5 commits into from May 22, 2012

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@libor-m

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

@jamescasbon
Owner

This is super cool, thanks very much.

I just need to check this out and update the tests, before it gets merged. Unless they are already passing?

@libor-m
@jamescasbon jamescasbon merged commit 30c71b6 into jamescasbon:master May 22, 2012
@jamescasbon
Owner

Hey @libor-m do you want to submit your filters for inclusion? Would be great to get them in before I cut the next release.

@libor-m

The filters I was using for my project are in https://github.com/libor-m/scrimer/blob/master/pyvcf_filters.py . Check them and if any of them seems sensible - and reuasble for the others - to you, you're welcome to include those in pyvcf.

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