fix 4648 #4670
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fix 4648 #4670
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Codecov Report
@@ Coverage Diff @@
## master #4670 +/- ##
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+ Coverage 79.835% 79.843% +0.008%
- Complexity 17328 17333 +5
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Files 1074 1074
Lines 62907 62921 +14
Branches 10181 10182 +1
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+ Hits 50222 50238 +16
Misses 8704 8704
+ Partials 3981 3979 -2
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cwhelan
approved these changes
Apr 19, 2018
| newTigStart = input.startInAssembledContig; | ||
| newTigEnd = input.endInAssembledContig - clipLengthOnRead; | ||
| newTigStart = originalContigStart; | ||
| newTigEnd = Math.min(originalContigEnd - clipLengthOnRead, |
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As discussed in person maybe add a couple of notes in comments to highlight why this is necessary?
* fixed bug in ref. span and read span when clipping alignment * add argument check in AlignmentInterval * correct invalid test data
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May 25, 2018
* fixed bug in ref. span and read span when clipping alignment * add argument check in AlignmentInterval * correct invalid test data
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fix #4648
The problems are in clipping the alignments when de-overlapping the alignments, particularly computing the new ref and read spans.
Also adds a check on arguments used for constructing alignments, which helped finding errors in test data (now corrected)