Most of the flagging code is looking for simple "hit" lookups in tabix files. This can be handled in exactly the same way as the input generation speed up.
Will have additional advantages as current code wraps each query with an eval which is expensive:
Should be able to hide this in the reuse_unmatched_normals_tabix and reuse_repeats_tabix functions. Needs to be applied in both FilterRules.pm and FragmentFilterRules.pm.
Most of the flagging code is looking for simple "hit" lookups in tabix files. This can be handled in exactly the same way as the input generation speed up.
Will have additional advantages as current code wraps each query with an
evalwhich is expensive:https://github.com/cancerit/cgpPindel/blob/da79133d7849117eca4ca3a22896d6b1256643b3/perl/lib/Sanger/CGP/PindelPostProcessing/FragmentFilterRules.pm#L339-L349
Should be able to hide this in the
reuse_unmatched_normals_tabixandreuse_repeats_tabixfunctions. Needs to be applied in bothFilterRules.pmandFragmentFilterRules.pm.