[ADAM-340] Adding the TrackedLayout trait and implementation. #341
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| ref1.overlaps(ref2) | ||
| } | ||
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| def recordSorter(rec1: ADAMRecord, rec2: ADAMRecord): Boolean = { |
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This object is otherwise generic; it seems like it'd be preferable to make this method generic such that any object that can emit a reference position can be sorted.
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Also, this method doesn't handle unaligned reads. I've opened a PR (broadinstitute#19) with a failing test.
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@fnothaft I think I've fixed your failing test, addressed your comment (above), and added some extra comments. Let me know what you think. |
OrderedTrackLayout is an implementation of TrackedLayout, which takes a sequence of Reference-mappable values and lays them out into tracks in a naive, order-dependent way.
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Looks good here! I presume this is rebased on master? |
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Yessir, it is. |
fnothaft
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Jul 30, 2014
[ADAM-340] Adding the TrackedLayout trait and implementation.
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Merged! Thanks @tdanford! |
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OrderedTrackLayout is an implementation of TrackedLayout, which takes a sequence of Reference-mappable values and lays them out into tracks in a naive, order-dependent way.