bcgsc/physlr issues and pull requests

#90 - read_tsv: accept graphs with no edge

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

#89 - typo fix

Pull Request - State: closed - Opened by aafshinfard about 5 years ago
Labels: bug

#88 - data: Download the fly genome from Ensembl

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

#87 - Brewfile: Add gnu-time miniasm pandoc pigz

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

#86 - physlr_remove_bridges_graph

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

#85 - fixed typo "prune_junctions"

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

#84 - separate --prune and --prune-bridges

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

#83 - Code cleaning

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

#82 - Fix a rare deadlock :D

Pull Request - State: closed - Opened by vlad0x00 about 5 years ago - 1 comment

#81 - Fix gap.bed error in data/Makefile

Pull Request - State: closed - Opened by janetxinli about 5 years ago - 3 comments
Labels: bug

#80 - determine_molecule: remove singletons afterward

Pull Request - State: closed - Opened by aafshinfard about 5 years ago
Labels: enhancement

#79 - Pylint errors

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

#78 - Option to filter minimizer with bloomfilter

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

#77 - pruning: weighted branch length

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

#77 - pruning: weighted branch length

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

#76 - determine_molecules: bug fix

Pull Request - State: closed - Opened by aafshinfard about 5 years ago - 1 comment
Labels: bug

#75 - physlr-filter-bxmx.cc: calculate high whisker correctly

Pull Request - State: closed - Opened by jwcodee about 5 years ago - 1 comment
Labels: invalid

#74 - Indexlr strand data update

Pull Request - State: closed - Opened by vlad0x00 about 5 years ago

#73 - Calculate tfidf

Pull Request - State: closed - Opened by MurathanGoktas about 5 years ago - 1 comment
Labels: Stale

#72 - Physlr: compute intersection of neighbour minimizers as edge weight

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

#71 - Fix pylint errors in physlr_paf_metrics

Pull Request - State: closed - Opened by lcoombe over 5 years ago - 1 comment

#70 - determine_molecules: bug fix

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: bug

#69 - physlr-indexlr: Fix --pos coordinates to include Ns

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: bug

#68 - physlr-indexlr: Optionally output minimizers positions

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: enhancement

#67 - src/include/: Reformat white space with clang-format

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

#66 - Remove thread option for now in overlap code

Pull Request - State: closed - Opened by JustinChu over 5 years ago - 8 comments

#65 - Fix an edge case bug

Pull Request - State: closed - Opened by vlad0x00 over 5 years ago - 5 comments

#64 - Reformat determine molecules

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 2 comments
Labels: enhancement

#63 - Extensive separation

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 4 comments
Labels: enhancement

#62 - determine_molecules: partition+cluster+merge

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 4 comments
Labels: enhancement

#61 - cosine sim bug fix

Pull Request - State: closed - Opened by aafshinfard over 5 years ago
Labels: bug

#60 - determine_molecules: optional squaring for cosine similarity

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 1 comment
Labels: enhancement

#59 - detect and remove junctions

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 2 comments
Labels: enhancement

#58 - refactor max-module-size

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

#57 - determine_molecules_k_clique_communities: Use extend

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

#56 - physlr_mst: integrate pruning

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: enhancement

#55 - cut-chimera: Cut chimeric paths to correct misassemblies

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: enhancement

#54 - Add src/data/f1.tiny.indexlr.physlr.tsv

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: bug

#53 - added sample test file

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 4 comments

#52 - Determine_molecules sub methods modularization

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 7 comments
Labels: enhancement

#51 - Pruned mst

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 4 comments
Labels: enhancement

#50 - reformatting of the code

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 1 comment

#49 - Check for white-space errors using clang-format

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 8 comments
Labels: enhancement

#48 - My benchmarking work

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 16 comments

#47 - Determine_molecules: Modularization + {Partition+Split+Merge}

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 6 comments
Labels: enhancement

#46 - Filter outlier barcodes-minimizers

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 30 comments
Labels: enhancement

#45 - Squaring and cosine similarity optimization

Issue - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: enhancement

#44 - map-mkt: Add heuristics to make it more scalable

Pull Request - State: closed - Opened by JustinChu over 5 years ago - 4 comments
Labels: enhancement

#43 - filter-barcodes: use robin-hash rather than stl

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 4 comments
Labels: enhancement

#42 - determine_molecules: strategy added: cosine of squared adj mat

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 13 comments
Labels: enhancement

#41 - Fix a deadlock

Pull Request - State: closed - Opened by vlad0x00 over 5 years ago - 1 comment
Labels: bug

#40 - src/Makefile: Add -Wno-error=unknown-pragmas to CXXFLAGS

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: bug

#39 - Update .gitignore

Pull Request - State: closed - Opened by vlad0x00 over 5 years ago - 2 comments

#38 - Use split minimizers for mapping

Pull Request - State: closed - Opened by lcoombe over 5 years ago - 2 comments
Labels: enhancement

#37 - add c++ overlap code

Pull Request - State: closed - Opened by JustinChu over 5 years ago
Labels: enhancement

#36 - determine_molecules: Louvain strategy added

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 6 comments
Labels: enhancement

#35 - Implementing igraph

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 5 comments
Labels: enhancement

#34 - Implementing IGraph

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 1 comment

#33 - determine-molecules: k-clique strategy added

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: enhancement

#32 - physlr-filter-barcodes: Time it

Pull Request - State: closed - Opened by gokcedilek over 5 years ago - 13 comments
Labels: enhancement

#31 - Use pigz for decompression as well

Pull Request - State: closed - Opened by vlad0x00 over 5 years ago
Labels: enhancement

#30 - "Options fixed, and added a sample test example to the src/makefile"

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

#29 - Parallelize physlr-filter-barcodes

Issue - State: closed - Opened by sjackman over 5 years ago - 3 comments
Labels: enhancement, Stale

#28 - physlr-filter-barcodes: Remove -k and -w options

Issue - State: closed - Opened by sjackman over 5 years ago - 4 comments
Labels: Stale

#27 - Azure: Run clang-tidy

Pull Request - State: closed - Opened by sjackman over 5 years ago
Labels: enhancement

#26 - subgraphs-stats

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 4 comments

#25 - compare-two-mol: compare 2 results based on a ref file

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: enhancement

#24 - compare-mol: Fix a bug

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: bug

#23 - fix in error message

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

#22 - Mol2bar comparison scripts

Pull Request - State: closed - Opened by aafshinfard over 5 years ago - 3 comments
Labels: enhancement

#21 - typo fix

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

#20 - bug fix, physlr_subgraphs

Pull Request - State: closed - Opened by aafshinfard almost 6 years ago - 4 comments
Labels: bug

#19 - Update nthash

Pull Request - State: closed - Opened by vlad0x00 almost 6 years ago - 1 comment
Labels: enhancement

#18 - Parallelize indexlr

Pull Request - State: closed - Opened by vlad0x00 almost 6 years ago - 23 comments
Labels: enhancement

#17 - fix, physlr_subgraphs

Pull Request - State: closed - Opened by aafshinfard almost 6 years ago - 1 comment
Labels: bug

#16 - physlr_subgraphs method

Pull Request - State: closed - Opened by aafshinfard almost 6 years ago - 2 comments
Labels: enhancement

#15 - Add physlr-filterbarcodes

Pull Request - State: closed - Opened by gokcedilek almost 6 years ago - 18 comments
Labels: enhancement

#14 - Scaffold trend mkt

Pull Request - State: closed - Opened by JustinChu almost 6 years ago - 5 comments
Labels: enhancement

#13 - molecules: Remove components of only one vertex

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

#12 - Bugfix to split-reads-molecules and minor Makefile edit

Pull Request - State: closed - Opened by lcoombe almost 6 years ago
Labels: bug

#11 - Fix python command

Pull Request - State: closed - Opened by ghost almost 6 years ago - 3 comments
Labels: bug, duplicate

#10 - A python invocation prefixed with a `time` command fails.

Pull Request - State: closed - Opened by ghost almost 6 years ago - 2 comments
Labels: bug

#9 - Given a dash ("-") in stead of input file, physlr-indexlr switches to reading cin.

Pull Request - State: closed - Opened by ghost almost 6 years ago - 2 comments
Labels: bug, enhancement

#8 - Adding code to split minimizers and reads by molecule

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 7 comments
Labels: enhancement

#7 - Add code to generate minimizers of a read using ntHash-2.0.0

Pull Request - State: closed - Opened by ghost almost 6 years ago - 48 comments
Labels: enhancement

#6 - Flesh backbone: Code style fixes and refactoring

Pull Request - State: closed - Opened by lcoombe almost 6 years ago - 1 comment
Labels: enhancement

#5 - Azure: Install networkx tqdm

Pull Request - State: closed - Opened by sjackman almost 6 years ago
Labels: bug

#4 - Add code to flesh out backbone

Pull Request - State: closed - Opened by lcoombe about 6 years ago - 3 comments
Labels: enhancement

GitHub / bcgsc/physlr issues and pull requests