https://github.com/genome/genome
Revision 9ba14039360c2facefb6cd56892084fe83ce8df5 authored by Dave Larson on 03 July 2013, 13:45:09 UTC, committed by Dave Larson on 03 July 2013, 13:51:49 UTC
to chromosomes 1-22, X, Y and MT. Obviously, this is not always desirable as all of our sequencing is not human and we occasionally have "extra" chromosomes that need to be included because we are looking for viruses. This commit does a few things: * Adds a DV2 filter called TigraValidationFull that attempts to run on any chromosomes in the fasta .fai file. There are probably better ways to find those chromosomes (examining the BAM header), but these changes were quick and aimed at addressing a current analysis project. This TigraValidationFull filter is needed to interact with BreakdancerMax that Scott recently committed to remove similar restrictions in BreakDancer's DV2 module. * Adds and option to G::M::T::BreakDancer::SplitFiles so that it optionally doesn't split its files by this same hardcoded chromosome list. TigraValidationFull uses this option to pick up the extra chromosomes. * Note that the test for TigraValidationFull is just a copy of the tests for the regular TigraValidation. Coverage of the new functionality is not included and is deferred for later.
1 parent 362be71
Tip revision: 9ba14039360c2facefb6cd56892084fe83ce8df5 authored by Dave Larson on 03 July 2013, 13:45:09 UTC
Our SV pipeline contains a number of places where output is restricted
Our SV pipeline contains a number of places where output is restricted
Tip revision: 9ba1403
Computing file changes ...