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jeromekelleher
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sc2ts
Infer a succinct tree sequence from SARS-COV-2 variation data
MIT License
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Pin zarr < 2.18
#192
szhan
closed
19 hours ago
0
Issue with zarr 2.18.2
#191
szhan
closed
19 hours ago
1
Dump pickled objects of samples filtered by HMM cost
#190
szhan
closed
19 hours ago
2
Filter samples by HMM cost without match grouping
#189
szhan
closed
22 hours ago
1
Identify sensible max HMM cost thresholds
#188
szhan
opened
1 day ago
1
Implement HMM cost to filter samples
#187
szhan
closed
1 week ago
2
Add details about copying path and mutations to node metadata
#186
szhan
closed
1 week ago
0
Negative submission delay
#185
szhan
closed
6 hours ago
7
Uppercase input sequences
#184
szhan
closed
2 months ago
0
Fast evaluation test for false positives
#183
hyanwong
opened
1 year ago
0
Excluding hypervariable sites?
#182
hyanwong
closed
1 year ago
1
Check QC filtering
#181
jeromekelleher
opened
1 year ago
0
Subgraph plotting: enhancement for showing mutations
#180
hyanwong
opened
1 year ago
0
Alternative/additional data filtering by HMM cost
#179
jeromekelleher
closed
1 week ago
10
Trivial tweak to separate adjoining interval labels
#178
hyanwong
closed
1 year ago
0
Allow numbers of descendant samples to be shown even on nonsample nodes
#177
hyanwong
closed
1 year ago
0
Record HMM details for every sample
#176
jeromekelleher
closed
1 week ago
7
Detect false recombinations by checking if we have mutations with very few inheritors
#175
jeromekelleher
opened
1 year ago
1
Detect false recombinations by mismatch in inheritors for parents
#174
jeromekelleher
opened
1 year ago
0
Correct call to sc2ts TreeInfo in utils.py
#173
hyanwong
closed
1 year ago
0
Compute "success" of inferred nodes
#172
jeromekelleher
opened
1 year ago
0
Move nextstrain code to paper repo
#171
jeromekelleher
opened
1 year ago
0
Ingest data from primary sources
#170
jeromekelleher
opened
1 year ago
0
Packaging stuff 2
#169
jeromekelleher
closed
1 year ago
0
Fix packaging issues
#168
jeromekelleher
closed
1 year ago
0
CLI tidyups
#167
jeromekelleher
closed
1 year ago
0
Tidy ups
#166
jeromekelleher
closed
1 year ago
0
numba warning: missing nopython argument
#165
hyanwong
closed
1 year ago
0
Need a requirements.txt file
#164
hyanwong
closed
1 year ago
0
Add the max genetic distance between parents at a breakpoint
#163
hyanwong
opened
1 year ago
0
Add interval computation
#162
jeromekelleher
closed
1 year ago
0
Remove 0 and L from recombinant breakpoints
#161
jeromekelleher
opened
1 year ago
0
Node with ARG breakpoint not present in either HMM run
#160
hyanwong
closed
1 year ago
4
Derive breakpoint interval by comparing parents
#159
jeromekelleher
opened
1 year ago
3
Preprocess daily batch to find identical sequences?
#158
jeromekelleher
opened
1 year ago
0
Minor util improvements
#157
hyanwong
closed
1 year ago
1
Make the core Wuhan node a sample
#156
hyanwong
opened
1 year ago
0
Ability to run a specific HMM match again?
#155
hyanwong
opened
1 year ago
6
XB parent copying unparsimonious
#154
hyanwong
opened
1 year ago
3
Minor logic correction in plot
#153
hyanwong
closed
1 year ago
0
sc2ts.initial_ts() doesn't mark 'Wuhan/Hu-1/2019' as a sample
#152
hyanwong
opened
1 year ago
5
Add internal sample stats to TreeInfo:
#151
hyanwong
opened
1 year ago
0
Add `dereference_singleton_recombinants`
#150
hyanwong
closed
1 year ago
2
Bug in `plot_subgraph`
#149
hyanwong
opened
1 year ago
0
Get the mutational spectrum of a specified node and its descendants
#148
szhan
opened
1 year ago
2
Better alignment of edge labels
#147
hyanwong
closed
1 year ago
1
Make plot_subgraph func
#146
hyanwong
closed
1 year ago
0
Limiting node expansion when getting a sample subgraph
#145
szhan
closed
1 year ago
2
Pluralization logic wrong way round
#144
hyanwong
closed
1 year ago
0
Rework sample_subgraph plot, particularly labels
#143
hyanwong
closed
1 year ago
11
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