WIP: Improve variant calling #4
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Needs testing on real genome. Needs code refactoring and cleanup.
…egrate Dominique's fix
… Need to check qor though.
…ot take into consideration the cases with multiple indels (pb with non increasing positions of indels). Also see some issue that some indels are still not detected, need to check.
…w I get the results in case of several indels. Will try to fix that
Some modifications in SW results read which I probably need to revert
Revert latest modifications in SW results parsing.
…or mapping filters
…ts of it with a python script
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There are quite a few things I still need to clean up: functions that could be merged, TODOs and FIXMEs to address, gotos to remove...