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Fix CRAM mismatches calculation regression in v2.2.0 #3342
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Codecov Report
@@ Coverage Diff @@
## main #3342 +/- ##
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- Coverage 59.16% 59.14% -0.03%
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Files 750 751 +1
Lines 29266 29270 +4
Branches 7084 7083 -1
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- Hits 17316 17312 -4
- Misses 11756 11764 +8
Partials 194 194
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now does a "cross-check" by comparing the CIGAR and mismatches data structures from the same data file encoded in BAM and CRAM this picked up a number of subtle logic bugs that were good to catch |
The PR at #3293 introduced a regression where CRAM mismatches would be calculated incorrectly with the 'i' readFeature type due to incorrectly assuming that readFeatures would have an indication of stretches of matches. This PR fixes that assumption using code similar to the CIGAR generation