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iqbal-lab-org
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make_prg
Code to create a PRG from a Multiple Sequence Alignment file
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Bump pillow from 10.2.0 to 10.3.0
#69
dependabot[bot]
opened
5 months ago
1
Bump black from 22.12.0 to 24.3.0
#68
dependabot[bot]
opened
5 months ago
0
Bump pyinstaller from 5.13.0 to 5.13.1
#67
dependabot[bot]
closed
7 months ago
1
Bump fonttools from 4.41.0 to 4.43.0
#66
dependabot[bot]
closed
7 months ago
1
Bump pillow from 10.0.0 to 10.2.0
#65
dependabot[bot]
closed
7 months ago
1
Bump pillow from 10.0.0 to 10.0.1
#64
dependabot[bot]
closed
7 months ago
2
v0.5.0 release
#63
leoisl
closed
1 year ago
1
Preparing v0.5.0 release
#62
leoisl
closed
1 year ago
5
Local random object and Skipping malformed denovo variants
#61
leoisl
closed
1 year ago
1
Properly handling Ns in make_prg
#60
leoisl
closed
1 year ago
2
Bump scipy from 1.9.3 to 1.10.0
#59
dependabot[bot]
closed
1 year ago
1
Ignore `N`s that might have slipped through when updating PRGs
#58
leoisl
opened
1 year ago
4
segfaulting when building from_msa
#57
iqbal-lab
opened
1 year ago
6
AssertionError: Each sequence should be in a cluster
#56
Danderson123
closed
1 year ago
1
Strange difference in overlapping positions between make_prg versions
#55
mbhall88
opened
1 year ago
11
Precompiled binary issue
#54
mbhall88
closed
1 year ago
6
Merge code for 0.4.0 release into master
#53
leoisl
closed
1 year ago
0
Embed mafft into make_prg
#52
leoisl
closed
1 year ago
4
Add --update-method to make_prg update
#51
leoisl
opened
1 year ago
1
MAFFT is portable for linux and we can embed it into make_prg
#50
leoisl
closed
1 year ago
4
Preparing 0.4.0 release
#49
leoisl
closed
1 year ago
0
Changing the node building priority in NodeFactory.build()
#48
leoisl
closed
1 year ago
2
Copy-on-write might not be efficient in python
#47
leoisl
opened
1 year ago
0
Implements update_shared_data as a class attribute in a singleton pattern and drops Mac OS X support
#46
leoisl
closed
1 year ago
3
Global variables, multiprocessing and pickling
#45
leoisl
closed
1 year ago
5
scikit-learn = "^1.0" makes integration tests get stuck
#44
leoisl
closed
1 year ago
8
Understand why latest executable of new make_prg version did not produce the expected graph
#43
leoisl
closed
1 year ago
1
make_prg update PR series: 7. Misc changes
#42
leoisl
closed
1 year ago
14
Recent version of pytest gets stuck on make_prg integration tests
#41
leoisl
closed
1 year ago
5
make_prg update PR series: 6. Add sample example and update tests
#40
leoisl
closed
1 year ago
2
Accept multiple suffixes for option -s / --suffix
#39
leoisl
opened
1 year ago
0
Handling "N" inputs in fasta file
#38
AlperYurtseven
closed
1 year ago
2
make_prg update PR series: 5. CLI changes
#37
leoisl
closed
1 year ago
2
make_prg update PR series: 4. make_prg update
#36
leoisl
closed
2 years ago
12
make_prg update PR series: 3. CLI changes
#35
leoisl
closed
2 years ago
7
make_prg update PR series: 2. make_prg/utils refactoring/updates
#34
leoisl
closed
2 years ago
1
make_prg update PR series: 1. make_prg/from_msa refactoring/updates
#33
leoisl
closed
2 years ago
2
Version/fork confusion
#32
kdm9
closed
1 year ago
11
Vcf output
#31
khodor14
closed
1 year ago
4
Input to make_prg
#30
khodor14
closed
1 year ago
5
Header of summary.tsv file
#29
gavinmdouglas
closed
2 years ago
2
Fix 27
#28
bricoletc
closed
2 years ago
6
Indels can cause spurious site production
#27
bricoletc
opened
2 years ago
2
Provide some options to reduce output files
#26
mbhall88
closed
2 years ago
5
Fix #24
#25
bricoletc
closed
3 years ago
0
Repeats can cause underclustering
#24
bricoletc
closed
3 years ago
0
GFA format and ML path format
#23
bricoletc
opened
3 years ago
1
Gramtools compatibility + clearer CLI and output files
#22
bricoletc
closed
3 years ago
6
Add dockerfile
#21
mbhall88
closed
3 years ago
1
Singularity container can't be run in snakemake pipelines
#20
leoisl
closed
1 year ago
2
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