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yatisht
/
usher
Ultrafast Sample Placement on Existing Trees
MIT License
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new options for matUtils extract: --max-mut-density, --node-stats
#278
AngieHinrichs
closed
1 year ago
2
Web USHeR -- dropdown to monkeypox not working
#277
sidneymbell
closed
1 year ago
4
Usher should accept EPI_SETs exported directly, recognize EPI_ISL_14884799-EPI_ISL_14884801
#276
corneliusroemer
closed
1 year ago
9
branch-specific masking: compare par_nuc not ref_nuc
#275
AngieHinrichs
closed
1 year ago
0
Parameters used in web version
#274
abulenciamiguel
closed
1 year ago
6
usher-sampled : Exit properly when there is no sample to place
#273
yceh
closed
1 year ago
0
modularize matOptimize for larch
#272
yceh
closed
1 year ago
0
Web Error: "Why did we not get EOF starting out with bignum"
#271
corneliusroemer
closed
1 year ago
3
TSV summary of sequences and placements output
#270
abulenciamiguel
closed
1 year ago
4
Small PR with improved error handling
#269
jmcbroome
closed
1 year ago
0
non-intuitive behavior for empty subsets, arguably a bug
#268
jbloom
closed
1 year ago
4
Usher not preserving the original tree topology
#267
cssmillie
opened
1 year ago
2
ENH: Add RKI (German) sequences that haven't yet been submitted to GISAID
#266
corneliusroemer
opened
1 year ago
0
Fix segv in matUtils summary -C when a node doesn't have the expected number of clade annotations
#265
AngieHinrichs
closed
1 year ago
0
usher-sampled support MAPLE input
#264
yceh
closed
1 year ago
0
ENH: Speed up Usher webversion
#263
corneliusroemer
closed
1 year ago
4
Fix missing internal node name in move log
#262
yceh
closed
1 year ago
0
Firefox Browser: Unsecure site
#261
FedeGueli
closed
1 year ago
8
Support Diff file from MAPLE
#260
yceh
closed
1 year ago
4
usher-sampled on empty tree and matutils extract with arbitrary length genome
#259
yceh
closed
1 year ago
0
try fix mac build
#258
yceh
closed
1 year ago
0
Ready to merge into the main branch
#257
yceh
closed
1 year ago
2
Fix segv when get_subtree is called without keep_clade_annotations on tree with annotations
#256
AngieHinrichs
closed
1 year ago
2
Make nodes with changed major allele set available to larch through the callback
#255
yceh
closed
1 year ago
3
Nearest neighbors / within-distance fix
#254
amkram
closed
1 year ago
0
Move found Callback
#253
yceh
closed
1 year ago
0
ENH: Add callback for discovered moves
#252
ognian-
closed
1 year ago
6
Add --within-distance to matUtils extract (output all samples within k mutations of target samples)
#251
amkram
closed
2 years ago
0
add simulation scripts
#250
bpt26
closed
2 years ago
0
ripples filtration pipeline scripts
#249
mrkylesmith
closed
2 years ago
0
Fix missing newline in placement stat when sample is filtered.
#248
yceh
closed
2 years ago
2
Usher sampled server [Experimental]
#247
yceh
closed
2 years ago
5
Bugfixes and set intersection refactor
#246
jmcbroome
closed
2 years ago
1
matUtils extract results in Segmentation Fault
#245
kvargha
closed
2 years ago
2
get_short_paths: intersect good_samples with samples_to_check using std::unordered_set
#244
AngieHinrichs
closed
2 years ago
0
matUtils extract --max-path-length includes samples that should be excluded by --max-parsimony, --max-branch-length
#243
AngieHinrichs
closed
2 years ago
5
Allow --clade-paths to work in conjunction with --clade-mutations and --clade-names
#242
AngieHinrichs
closed
2 years ago
0
Fix removal of newick sequence absent in vcf near root
#241
yceh
closed
2 years ago
0
output protobuf instead of newick when drifting
#240
yceh
closed
2 years ago
0
Web UShER unhandled failure
#239
rkdover
closed
1 year ago
3
Docker UShER exits printing "Killed"
#238
rkdover
closed
2 years ago
2
Resolve endless loop on TB
#237
yceh
closed
2 years ago
0
Same Node, Different Lineage
#236
ktmeaton
opened
2 years ago
5
Recombinant lineage nomenclature miscBA1BA2PostX
#235
ktmeaton
opened
2 years ago
8
Fix indexing bug that can cause overspecific clade assignment
#234
AngieHinrichs
closed
2 years ago
1
indexing bug can cause overspecific clade assignment
#233
AngieHinrichs
closed
2 years ago
0
Minor bugfixes and reorganizing some source code
#232
jmcbroome
closed
2 years ago
0
Possible issue with AT.1 lineage path
#231
joshuailevy
opened
2 years ago
6
BUG: Web usher sometimes crashes with `menuparent" id="myData">My Data`
#230
corneliusroemer
opened
2 years ago
0
Small pull request including bugfix and JSON filtering
#229
jmcbroome
closed
2 years ago
0
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