Closed standage closed 5 years ago
Merging #366 into master will increase coverage by
0.02%
. The diff coverage is90.91%
.
@@ Coverage Diff @@
## master #366 +/- ##
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+ Coverage 96.83% 96.85% +0.02%
==========================================
Files 48 48
Lines 2906 2923 +17
Branches 538 543 +5
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+ Hits 2814 2831 +17
Misses 58 58
Partials 34 34
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/alac.py | 98.18% <ø> (ø) |
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kevlar/call.py | 97.17% <100%> (+2.02%) |
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kevlar/cli/alac.py | 100% <100%> (ø) |
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kevlar/cli/call.py | 100% <100%> (ø) |
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kevlar/varmap.py | 99.05% <100%> (+0.03%) |
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kevlar/vcf.py | 92.76% <71.43%> (-0.57%) |
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The
--max-diff
setting in thelocalize
module has been in place for a while, and determines the distance required between adjacent seed matches to split a reference target into multiple targets. It is effective when a contig maps to multiple locations and kevlar needs to distinguish the optimal alignment(s) for variant calling.However, in some exceptional cases the reference target includes an array of tandem repeats that spans a huge genomic interval. Each repeat unit is separated by several kilobases, small enough that two adjacent units are not split by the
--max-diff
setting. Reducing the--max-diff
setting to filter out these loci would compromise kevlar's ability to capture large indels.This update introduces a complementary filter to discard unreasonably long reference targets that introduce tremendous performance problems at the alignment/calling step. Any reference target longer than L bp (default=10kb) will be discarded, and the associated contig will be reported in the VCF with no genomic position.
This update also includes the latest results from simulation experiments.