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cancerit / cgpCaVEManWrapper

Reference implementation of CGP workflow for CaVEMan SNV analysis
http://cancerit.github.io/cgpCaVEManWrapper/
GNU Affero General Public License v3.0
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noflag option addition results in loss of flagged VCF file #27

Closed keiranmraine closed 8 years ago

keiranmraine commented 8 years ago

Condition for moving data around is incorrect here:

https://github.com/cancerit/cgpCaVEManWrapper/blob/590e60e6ce9f76081ce52c8e6ae7958e65ad78ed/bin/caveman.pl#L211

The logic looks like it should match this:

https://github.com/cancerit/cgpCaVEManWrapper/blob/590e60e6ce9f76081ce52c8e6ae7958e65ad78ed/bin/caveman.pl#L167

For sanity/simplification suggest pre-processing option so [un]defined checks aren't necessary:

 $opts{'noflag'} = 0 unless(defined $opts{'noflag'});

somewhere around:

https://github.com/cancerit/cgpCaVEManWrapper/blob/590e60e6ce9f76081ce52c8e6ae7958e65ad78ed/bin/caveman.pl#L302