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kevlar-dev
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kevlar
Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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Update to homopolymer filter
#338
standage
closed
5 years ago
1
Fix bug with merging variants
#337
standage
closed
5 years ago
1
Filter short indels abutting homopolymers
#336
standage
closed
5 years ago
1
Sandbox scripts
#335
standage
closed
5 years ago
1
Utility scripts
#334
standage
closed
5 years ago
0
Homopolymer filter
#333
standage
closed
5 years ago
0
Handle multinucleotide variants correctly
#332
standage
closed
5 years ago
1
Adjacent SNVs (multinucleotide variants) called incorrectly
#331
standage
closed
5 years ago
0
Clean up `get_abundances` function
#330
standage
closed
5 years ago
0
Bring varfilter into Snakemake workflow
#329
standage
closed
5 years ago
0
Speed up simlike by skipping calculations for filtered variants
#328
standage
closed
5 years ago
2
Introduce --ctrl-max heurisitic at simlike stage
#327
standage
closed
5 years ago
1
Dynamically compute length of output for functional test
#326
standage
closed
5 years ago
1
Normalize likelihood scores by number of spanning k-mers
#325
standage
closed
5 years ago
1
Skip likelihood score calculation for some filtered calls
#324
standage
closed
5 years ago
0
Investigate --ctrl-max as a heuristic when calculating likelihood score
#323
standage
closed
5 years ago
0
Update filter command in workflow Mark I
#322
standage
closed
5 years ago
1
Logging updates
#321
standage
closed
5 years ago
1
Update workflow Mark I to match updates to filter module
#320
standage
closed
5 years ago
0
The state of the log
#319
standage
closed
5 years ago
0
New "varfilter" module
#318
standage
closed
5 years ago
0
Window check bugfix
#317
standage
closed
5 years ago
1
Split filter module functionality
#316
standage
closed
5 years ago
1
Split out functionality of filter module
#315
standage
closed
5 years ago
1
Split workflow
#314
standage
closed
5 years ago
1
Simlike bug fix for short reference window
#313
standage
closed
5 years ago
1
Minor updates to workflow Mark I
#312
standage
closed
5 years ago
1
Check size of reference window in simlike
#311
standage
closed
5 years ago
1
Put `--include` parameter value in single quotes in workflow Mark I
#310
standage
closed
5 years ago
0
Fix logging in assembly module
#309
standage
closed
5 years ago
0
Huge update to logging code
#308
standage
closed
5 years ago
2
Refactor logging code
#307
standage
closed
5 years ago
0
New workflow (mark I)
#306
standage
closed
5 years ago
1
New workflow for preprocessing BAM data
#305
standage
closed
5 years ago
2
Fix erroneous contig attribute with indels
#304
standage
closed
5 years ago
1
Discard short alignment blocks prior to variant calling
#303
standage
closed
5 years ago
1
Extend variant-spanning-kmer-mask capability to `kevlar call`
#302
standage
closed
5 years ago
1
Updates to localize & alac modules
#301
standage
closed
5 years ago
1
Updates to documentation
#300
standage
closed
5 years ago
1
Logging improvements for v0.6 release
#299
standage
closed
5 years ago
2
Logging improvements
#298
standage
closed
5 years ago
2
Things to deprecate
#297
standage
closed
5 years ago
0
Update docs
#296
standage
closed
5 years ago
0
Add --gen-mask flag to `kevlar call`
#295
standage
closed
5 years ago
0
Refactor code for assembly, localization, and calling
#294
standage
closed
5 years ago
1
[WIP] Fix erroneously filtered indel call
#293
standage
closed
5 years ago
2
Improved logging, fixed --gen-mask bug
#292
standage
closed
5 years ago
1
Fix sketch memory when using non-byte counter
#291
standage
closed
5 years ago
1
Incorrect table sizes in `kevlar count`
#290
standage
closed
5 years ago
0
Generate a mask from variant-spanning k-mers
#289
standage
closed
5 years ago
1
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