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waveygang
/
wfmash
base-accurate DNA sequence alignments using WFA and mashmap2
MIT License
172
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15
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allow only creating the index and exiting
#257
ekg
closed
1 week ago
0
expose min inversion patch length on CLI
#256
ekg
closed
1 week ago
0
Inversion patching
#255
ekg
closed
1 week ago
3
Read/write index
#254
bkille
closed
1 week ago
0
Fix SAM format output and HARD clipping
#253
AndreaGuarracino
closed
1 week ago
0
Avoid division by 0 to determine `minhash_kmer_size`
#252
AndreaGuarracino
closed
2 weeks ago
0
Assertion `queryLen <= querySize' failed
#251
shuai19910911
opened
2 weeks ago
0
Illegal Instruction: wfmash:0.14.0 bioconda on linux container
#250
msgr0
opened
3 weeks ago
4
BUILD_STATIC not used
#249
pickettbd
opened
3 weeks ago
0
Stampede3 build
#248
ekg
closed
3 weeks ago
0
scoring parameter updates for broader diversity and alignment mode optimizations
#247
ekg
closed
3 weeks ago
2
optionally force global biwfa alignment of mappings
#246
ekg
closed
1 month ago
0
random access to queries when aligning
#245
ekg
closed
1 month ago
0
should query range be expanded for head/tail patching?
#244
ekg
opened
1 month ago
0
reimplement static builds
#243
ekg
closed
1 month ago
0
Specify queries
#242
ekg
closed
1 month ago
3
wfmash seems much slower in `-Y #` mode compared to `-X`, although the input follows the PanSN-spec
#241
subwaystation
opened
1 month ago
0
Fix freq seed count
#240
bkille
closed
2 weeks ago
0
Handle thread output incrementally
#239
bkille
closed
2 weeks ago
0
for the chain_gap, do not go above 20k by default
#238
AndreaGuarracino
closed
2 months ago
0
queryLen <= querySize failed of wfmash
#237
baozg
closed
2 months ago
2
improve MAC compatibility
#236
AndreaGuarracino
closed
2 months ago
1
fix "alignment block length" in PAF output
#235
AndreaGuarracino
closed
2 months ago
0
Make chain gap dynamic
#234
bkille
closed
2 months ago
1
Is linear synteny assumed?
#233
rsharris
opened
3 months ago
8
Problem installing wfmash with conda on mac
#232
rsharris
opened
3 months ago
5
drop timing from the output by default
#231
AndreaGuarracino
closed
3 months ago
0
parameter check for WFA?
#230
vpbrendel
opened
3 months ago
4
Convex penalties for the alignment patching
#229
AndreaGuarracino
closed
3 months ago
0
Tune patching
#228
AndreaGuarracino
closed
3 months ago
1
too many alignments with v0.12.6
#227
subwaystation
opened
4 months ago
20
return 1.0d ?
#226
NullModel
closed
2 months ago
1
Do not allow a segment to chain with itself
#225
bkille
closed
4 months ago
0
wfmash killed
#224
mictadlo
opened
4 months ago
0
Custom tags explanation
#223
sivico26
opened
5 months ago
1
make the script more robust
#222
AndreaGuarracino
closed
5 months ago
0
v0.12.5 emits more tabs than expected
#221
subwaystation
opened
5 months ago
2
Don't include endpoint in L2 range
#220
bkille
closed
5 months ago
0
Add error when the index is empty
#219
bkille
closed
5 months ago
0
`Floating point exception (core dumped)`
#218
subwaystation
closed
5 months ago
2
Enable one to one filtering
#217
bkille
closed
6 months ago
0
add `guix.scm`
#216
AndreaGuarracino
closed
7 months ago
1
Don't use hypergeometric model for low-complexity segments.
#215
bkille
closed
6 months ago
2
Average kmer complexities over chain in mergeMappingsInRange
#214
bkille
closed
7 months ago
0
All outputs in [0, 1] now (again)
#213
bkille
closed
7 months ago
0
fix id representation
#212
AndreaGuarracino
closed
7 months ago
0
Output ANI in [0, 1] instead of [0, 100]
#211
bkille
closed
7 months ago
0
Initialize stage2 scan flag
#210
bkille
closed
7 months ago
0
fix unset variable
#209
AndreaGuarracino
closed
7 months ago
0
Disable random dropping (for now)
#208
AndreaGuarracino
closed
7 months ago
0
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