iqbal-lab-org/make_prg issues and pull requests

#69 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: open - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#68 - Bump black from 22.12.0 to 24.3.0

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#67 - Bump pyinstaller from 5.13.0 to 5.13.1

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#66 - Bump fonttools from 4.41.0 to 4.43.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#65 - Bump pillow from 10.0.0 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: dependencies

#64 - Bump pillow from 10.0.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 2 comments
Labels: dependencies

#63 - v0.5.0 release

Pull Request - State: closed - Opened by leoisl over 1 year ago - 1 comment

#62 - Preparing v0.5.0 release

Pull Request - State: closed - Opened by leoisl over 1 year ago - 5 comments

#61 - Local random object and Skipping malformed denovo variants

Pull Request - State: closed - Opened by leoisl over 1 year ago - 1 comment

#60 - Properly handling Ns in make_prg

Pull Request - State: closed - Opened by leoisl over 1 year ago - 2 comments

#59 - Bump scipy from 1.9.3 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#58 - Ignore `N`s that might have slipped through when updating PRGs

Issue - State: open - Opened by leoisl over 1 year ago - 4 comments

#57 - segfaulting when building from_msa

Issue - State: open - Opened by iqbal-lab over 1 year ago - 6 comments

#56 - AssertionError: Each sequence should be in a cluster

Issue - State: closed - Opened by Danderson123 over 1 year ago - 1 comment

#55 - Strange difference in overlapping positions between make_prg versions

Issue - State: open - Opened by mbhall88 almost 2 years ago - 11 comments

#54 - Precompiled binary issue

Issue - State: closed - Opened by mbhall88 almost 2 years ago - 6 comments

#53 - Merge code for 0.4.0 release into master

Pull Request - State: closed - Opened by leoisl almost 2 years ago
Labels: updatable_graphs

#52 - Embed mafft into make_prg

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 4 comments
Labels: updatable_graphs

#51 - Add --update-method to make_prg update

Issue - State: open - Opened by leoisl almost 2 years ago - 1 comment

#50 - MAFFT is portable for linux and we can embed it into make_prg

Issue - State: closed - Opened by leoisl almost 2 years ago - 4 comments

#49 - Preparing 0.4.0 release

Pull Request - State: closed - Opened by leoisl almost 2 years ago
Labels: updatable_graphs

#48 - Changing the node building priority in NodeFactory.build()

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 2 comments
Labels: updatable_graphs

#47 - Copy-on-write might not be efficient in python

Issue - State: open - Opened by leoisl almost 2 years ago

#46 - Implements update_shared_data as a class attribute in a singleton pattern and drops Mac OS X support

Pull Request - State: closed - Opened by leoisl almost 2 years ago - 3 comments
Labels: updatable_graphs

#45 - Global variables, multiprocessing and pickling

Issue - State: closed - Opened by leoisl about 2 years ago - 5 comments

#44 - scikit-learn = "^1.0" makes integration tests get stuck

Issue - State: closed - Opened by leoisl about 2 years ago - 8 comments

#43 - Understand why latest executable of new make_prg version did not produce the expected graph

Issue - State: closed - Opened by leoisl about 2 years ago - 1 comment

#42 - make_prg update PR series: 7. Misc changes

Pull Request - State: closed - Opened by leoisl about 2 years ago - 14 comments
Labels: updatable_graphs

#41 - Recent version of pytest gets stuck on make_prg integration tests

Issue - State: closed - Opened by leoisl about 2 years ago - 5 comments

#40 - make_prg update PR series: 6. Add sample example and update tests

Pull Request - State: closed - Opened by leoisl about 2 years ago - 2 comments
Labels: updatable_graphs

#39 - Accept multiple suffixes for option -s / --suffix

Issue - State: open - Opened by leoisl about 2 years ago

#38 - Handling "N" inputs in fasta file

Issue - State: closed - Opened by AlperYurtseven about 2 years ago - 2 comments

#37 - make_prg update PR series: 5. CLI changes

Pull Request - State: closed - Opened by leoisl over 2 years ago - 2 comments
Labels: updatable_graphs

#36 - make_prg update PR series: 4. make_prg update

Pull Request - State: closed - Opened by leoisl almost 3 years ago - 12 comments
Labels: updatable_graphs

#35 - make_prg update PR series: 3. CLI changes

Pull Request - State: closed - Opened by leoisl almost 3 years ago - 7 comments
Labels: updatable_graphs

#34 - make_prg update PR series: 2. make_prg/utils refactoring/updates

Pull Request - State: closed - Opened by leoisl almost 3 years ago - 1 comment
Labels: updatable_graphs

#33 - make_prg update PR series: 1. make_prg/from_msa refactoring/updates

Pull Request - State: closed - Opened by leoisl almost 3 years ago - 2 comments
Labels: updatable_graphs

#32 - Version/fork confusion

Issue - State: closed - Opened by kdm9 about 3 years ago - 11 comments

#31 - Vcf output

Issue - State: closed - Opened by khodor14 about 3 years ago - 4 comments

#30 - Input to make_prg

Issue - State: closed - Opened by khodor14 about 3 years ago - 5 comments

#29 - Header of summary.tsv file

Issue - State: closed - Opened by gavinmdouglas about 3 years ago - 2 comments

#28 - Fix 27

Pull Request - State: closed - Opened by bricoletc about 3 years ago - 6 comments

#27 - Indels can cause spurious site production

Issue - State: open - Opened by bricoletc about 3 years ago - 2 comments
Labels: bug

#26 - Provide some options to reduce output files

Pull Request - State: closed - Opened by mbhall88 about 3 years ago - 5 comments

#25 - Fix #24

Pull Request - State: closed - Opened by bricoletc over 3 years ago

#24 - Repeats can cause underclustering

Issue - State: closed - Opened by bricoletc over 3 years ago
Labels: bug

#23 - GFA format and ML path format

Issue - State: open - Opened by bricoletc over 3 years ago - 1 comment

#22 - Gramtools compatibility + clearer CLI and output files

Pull Request - State: closed - Opened by bricoletc almost 4 years ago - 6 comments

#21 - Add dockerfile

Pull Request - State: closed - Opened by mbhall88 almost 4 years ago - 1 comment

#20 - Singularity container can't be run in snakemake pipelines

Issue - State: closed - Opened by leoisl about 4 years ago - 2 comments

#19 - Refactored clustering code and new kmeans clustering criterion

Pull Request - State: closed - Opened by bricoletc about 4 years ago

#18 - Dev

Pull Request - State: closed - Opened by bricoletc over 4 years ago - 1 comment

#17 - Stop producing empty alleles

Issue - State: open - Opened by bricoletc over 4 years ago - 2 comments

#16 - add singularity image and update README

Pull Request - State: closed - Opened by mbhall88 over 4 years ago - 1 comment

#15 - Ambiguous path production

Issue - State: open - Opened by bricoletc over 4 years ago - 55 comments

#14 - Bugfix: erroneous clustering error raising

Pull Request - State: closed - Opened by bricoletc over 4 years ago

#13 - Refactoring and more unit tests

Pull Request - State: closed - Opened by bricoletc over 4 years ago - 2 comments
Labels: bug, enhancement

#12 - Incomplete ambiguous dna expansion

Issue - State: closed - Opened by bricoletc over 4 years ago - 1 comment

#11 - Viral alignments often have long runs of NNNs in...

Pull Request - State: closed - Opened by rmcolq almost 5 years ago - 3 comments

#10 - Add fasta header to PRG file

Pull Request - State: closed - Opened by mbhall88 about 5 years ago - 1 comment

#9 - Make output fasta formatted

Issue - State: closed - Opened by mbhall88 about 5 years ago

#8 - Refactoring and improving test coverage

Pull Request - State: closed - Opened by mbhall88 about 5 years ago - 2 comments

#7 - Should lowercase valid base raise error

Issue - State: closed - Opened by mbhall88 about 5 years ago - 3 comments

#6 - Reorganise with setup py

Pull Request - State: closed - Opened by martinghunt about 5 years ago

#5 - Feed gramtools + Fix #4

Pull Request - State: closed - Opened by bricoletc about 5 years ago - 2 comments

#4 - Tests fail if compiler reorders alleles

Issue - State: closed - Opened by rmcolq over 5 years ago

#3 - update default max nesting level

Pull Request - State: closed - Opened by mbhall88 over 5 years ago

#2 - kmer ID attribution

Issue - State: closed - Opened by leoisl over 5 years ago - 6 comments

#1 - increase default memory allocation

Pull Request - State: closed - Opened by mbhall88 almost 6 years ago - 2 comments

GitHub / iqbal-lab-org/make_prg issues and pull requests