Assembly-based realignment filter #6143
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takutosato
approved these changes
Sep 11, 2019
| final List<OverlapDetector<BwaMemAlignment>> overlapDetectors = new ArrayList<>(); | ||
| for (final List<BwaMemAlignment> unitigAlignments : allUnitigAlignments) { | ||
| final List<SimpleInterval> intervals = unitigAlignments.stream().map(RealignmentEngine::convertToInterval).collect(Collectors.toList()); | ||
| final OverlapDetector<BwaMemAlignment> overlapDetector = new OverlapDetector<BwaMemAlignment>(-maxReasonableFragmentLength/2, -maxReasonableFragmentLength/2); |
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Intellij: new OverlapDetector<BwaMemAlignment> -> new OverlapDetector<>
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Closes #6030.
@takutosato This a complete rewrite of the realignment filter, so I would review
FilterAlignmentArtifactsand its engine from scratch, not from the diff.There's still a bit of tuning to be done, but it's already far superior to the old version and I want to be using the release jar as much as possible for MC3.