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yatisht
/
usher
Ultrafast Sample Placement on Existing Trees
MIT License
120
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40
forks
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Question/discussion about low coverage samples
#328
theosanderson
closed
1 year ago
3
Fix diff loading with protobuf input
#327
yceh
closed
1 year ago
0
haplotypes gives mutations and their reversions in `matUtils summary --haplotype`
#326
jbloom
closed
1 year ago
5
Imputation and null genotypes/indels
#325
martinghunt
opened
1 year ago
10
an automated way of identifying masked sites?
#324
jbloom
closed
1 year ago
6
matOptimize sometimes failing when --vcf used
#323
martinghunt
closed
1 year ago
5
pre-built mutation annotated tree README doesn't link to correct references
#322
jbloom
opened
1 year ago
1
On dev server: `Warning/Error(s): Stack overflow in jsonWritePush`
#321
corneliusroemer
closed
1 year ago
1
fix reading empty vcf
#320
yceh
closed
1 year ago
0
Update link to license in README.md
#319
aofarrel
closed
1 year ago
0
¿Is UShER specific for SARS-CoV-2 or does it work with other viral organism sequences?
#318
AndreaAguadoM
closed
1 year ago
3
Bugfix and Reorganization
#317
jmcbroome
closed
1 year ago
2
removed "-defaults" channel
#316
russcd
closed
1 year ago
1
[possible bug] codons with two changes are not properly handled
#315
rneher
closed
1 year ago
1
masking of C21575T?
#314
jbloom
closed
1 year ago
2
Fix negative parsimony threshold
#313
yceh
closed
1 year ago
0
bug in counting of mutations at site 95 in 21J clade
#312
jbloom
closed
1 year ago
3
Disable ripple-fast vectorization on ARM
#311
yceh
closed
1 year ago
1
bioconda mac build fails for ripples-fast due to __builtin_ia32 instructions
#310
AngieHinrichs
opened
1 year ago
0
collapse_tree: preserve order expected by add_mutation
#309
AngieHinrichs
closed
1 year ago
1
bug: collapse_tree (matUtils extract -O) drops mutation in rare case
#308
AngieHinrichs
closed
1 year ago
0
Fix race condition when placing sample
#307
yceh
closed
1 year ago
0
Use at least 2 threads for usher-sampled
#306
yceh
closed
1 year ago
1
only request read permission on sample file
#305
yceh
closed
1 year ago
0
subtree extraction server and mutation path fix
#304
yceh
closed
1 year ago
1
Nextstrain-compatible JSON subtrees are now missing key: "value" pairs
#303
mdperry
opened
1 year ago
11
usher-server reload fix and add version string
#302
yceh
closed
1 year ago
0
Do the pre-built `UShER` trees mis-categorize 21L sequences as 21M?
#301
jbloom
closed
1 year ago
3
Add column of number of samples of query in subtree
#300
corneliusroemer
opened
1 year ago
0
Call the largest subtree number 1
#299
corneliusroemer
opened
1 year ago
3
Please show details even when >100 sequences are uploaded
#298
corneliusroemer
opened
1 year ago
2
Add `Pango lineage assigned by Usher` etc as colorings/metadata also for uploaded samples
#297
corneliusroemer
opened
1 year ago
3
Test web usher is broken: `ERR_EMPTY_RESPONSE`
#296
corneliusroemer
closed
1 year ago
4
add missing fclose
#295
yceh
closed
1 year ago
0
usher-server auto-reload
#294
yceh
closed
1 year ago
0
Add --no-ignore-prefix to usher-sampled (from usher-sampled-server)
#293
AngieHinrichs
closed
1 year ago
0
Handle empty tree and compatibility changes
#292
yceh
closed
1 year ago
0
Ancestral node VCFs
#291
lenorakepler
closed
1 year ago
2
fixed ripples-fast segfault with -s option
#290
mrkylesmith
closed
1 year ago
0
fix ripples-fast segfault with -s option
#289
mrkylesmith
closed
1 year ago
1
Fix subtree extraction && fork for newick writing
#288
yceh
closed
1 year ago
0
fixes date range for introduce clusters
#287
jen-martin
closed
1 year ago
0
miscellaneous small changes
#286
AngieHinrichs
closed
1 year ago
0
ENH: Zoom Auspice into uploaded node, to make it easier to immediately see where your sample is
#285
corneliusroemer
closed
1 year ago
1
ENH: Give internal nodes ids, so they can be labelled in Nextstrain URL
#284
corneliusroemer
closed
1 year ago
5
fix missing node names and incomplete extracted trees in usher-sampled
#283
yceh
closed
1 year ago
1
Test server issue
#282
corneliusroemer
closed
1 year ago
1
matUtils introduce: possible bug in handling cluster date range
#281
jen-martin
closed
1 year ago
2
Fix vcf loader segfault
#280
yceh
closed
1 year ago
1
fix missing file for usher-sampled-server
#279
yceh
closed
1 year ago
0
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