ffd61f4c1c
Eric reported this bug due to the reduced reads failing with an index out of bounds on what we thought was a deletion, but turned out to be a read starting with insertion. * Refactored PileupElement to distinguish clearly between deletions and read starting with insertion * Modified ExtendedEventPileup to correctly distinguish elements with deletion when creating new pileups * Refactored most of the lazyLoadNextAlignment() function of the LocusIteratorByState for clarity and to create clear separation between what is a pileup with a deletion and what's not one. Got rid of many useless if statements. * Changed the way LocusIteratorByState creates extended event pileups to differentiate between insertions in the beginning of the read and deletions. * Every deletion now has an offset (start of the event) * Fixed bug when LocusITeratorByState found a read starting with insertion that happened to be a reduced read. * Separated the definitions of deletion/insertion (in the beginning of the read) in all UG annotations (and the annotator engine). * Pileup depth of coverage for a deleted base will now return the average coverage around the deletion. * Indel ReadPositionRankSum test now uses the deletion true offset from the read, changed all appropriate md5's * The extra pileup elements now properly read by the Indel mode of the UG made any subsequent call have a different random number and therefore all RankSum tests have slightly different values (in the 10^-3 range). Updated all appropriate md5s after extremely careful inspection -- Thanks Ryan! phew! |
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