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@@ Coverage Diff @@
## master #28 +/- ##
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- Coverage 74.71% 66.79% -7.92%
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Files 1 1
Lines 1574 1801 +227
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+ Hits 1176 1203 +27
- Misses 398 598 +200
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update to gr.findoverlaps(by = ...). Much more efficient for big queries to be matched per levels specified in "by" metadata field. Previously, by queries first search for all possible overlaps and then filters on matching by queries. The newer implementation uses constructor function gr_construct_by which enables findOverlaps to search for overlaps only within factor levels rather than post-filtering.
Also added gaps functionality for GRangesLists. gr.setdiff2(by = ...) makes use of both gaps with grangeslists and also the new by implementation. New method gr.spreduce reduces by levels of a metadata field.
Also gr.start, gr.end, gr.flipstrand, are all now modified to work with grangeslists