92c5635e19
-- All functions tested. In the testing / review I discovered several bugs in the ActiveRegion routines that manipulate reads. New version should be correct -- Enforce correct ordering of supporting states in constructor -- Enforce read ordering when adding reads to an active region in add -- Fix bug in HaplotypeCaller map with new updating read spans. Now get the full span before clipping down reads in map, so that variants are correctly placed w.r.t. the full reference sequence -- Encapsulate isActive field with an accessor function -- Make sure that all state lists are unmodifiable, and that the docs are clear about this -- ActiveRegion equalsExceptReads is for testing only, so make it package protected -- ActiveRegion.hardClipToRegion must resort reads as they can become out of order -- Previous version of HC clipped reads but, due to clipping, these reads could no longer overlap the active region. The old version of HC kept these reads, while the enforced contracts on the ActiveRegion detected this was a problem and those reads are removed. Has a minor impact on PLs and RankSumTest values -- Updating HaplotypeCaller MD5s to reflect changes to ActiveRegions read inclusion policy |
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