Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bcgsc/physlr issues and pull requests

#196 - Support/distinction of other linked-read technologies

Issue - State: closed - Opened by pdimens about 1 month ago - 7 comments

#195 - Error 137?

Issue - State: open - Opened by YingChen94 3 months ago - 3 comments

#194 - Cannot install with Conda + Pypy 3.9

Issue - State: closed - Opened by davidlougheed 6 months ago - 3 comments

#193 - Question on 10x Genomics data

Issue - State: closed - Opened by YingChen94 6 months ago - 5 comments

#192 - filter-edges-m

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

#191 - indexlr long reads

Pull Request - State: closed - Opened by aafshinfard over 1 year ago
Labels: enhancement

#190 - indexlr-inputs

Pull Request - State: closed - Opened by aafshinfard over 1 year ago
Labels: enhancement

#189 - Btllib ci test

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

#188 - update dependencies

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

#187 - missing r packages

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

#186 - btllib

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

#185 - Long reads

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

#184 - fix readme info (#181)

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

#183 - fix readme info (#181)

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

#182 - AttributeError: module 'scipy.sparse' has no attribute 'coo_array'

Issue - State: open - Opened by aafshinfard over 2 years ago - 6 comments
Labels: Stale

#181 - fix readme info

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#180 - Improve readme

Pull Request - State: closed - Opened by aafshinfard over 2 years ago - 1 comment
Labels: enhancement

#179 - minor bug fix

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#178 - GitHub workflows

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#177 - v1.0.2 ready

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#176 - happy conda osx tests

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#175 - Logo

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

#174 - Physlr now published

Pull Request - State: closed - Opened by aafshinfard over 2 years ago

#173 - v1.0.1 ready

Pull Request - State: closed - Opened by aafshinfard over 2 years ago - 1 comment

#172 - Update README.md

Pull Request - State: closed - Opened by aafshinfard over 2 years ago - 1 comment

#171 - Add additional includes to physlr-molecules.cc

Pull Request - State: closed - Opened by kcleal over 3 years ago - 3 comments
Labels: Stale

#170 - Update README.md

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

#169 - Parameters for f1chr4 example?

Issue - State: closed - Opened by evolgenomics over 3 years ago - 5 comments
Labels: Stale

#168 - limit thread count for python mol-sep

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

#167 - V1.0.0 fixes

Pull Request - State: closed - Opened by aafshinfard over 3 years ago - 2 comments
Labels: bug

#166 - Corrections to README

Pull Request - State: closed - Opened by lcoombe about 4 years ago - 2 comments

#165 - Switch indexlr and makebf to btllib

Pull Request - State: closed - Opened by vlad0x00 about 4 years ago - 1 comment
Labels: Stale

#164 - Annotate graph bxmap

Pull Request - State: closed - Opened by aafshinfard about 4 years ago
Labels: enhancement

#163 - fix typo

Pull Request - State: closed - Opened by aafshinfard about 4 years ago - 1 comment

#162 - physlr-makebf: fix bug when reading file from stream

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

#161 - Physlr subgraph enable d

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

#160 - weighted branch depth

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

#159 - molecules.cc: cosine sim + iterative

Pull Request - State: closed - Opened by aafshinfard over 4 years ago - 3 comments
Labels: enhancement

#158 - Cosine sim

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

#157 - Make subgraph c++

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

#156 - Omp and binning c++

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

#155 - Make subgraph c++

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

#154 - Physlr molecules omp

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

#153 - doing nothing if u is not among junctions

Pull Request - State: closed - Opened by aafshinfard over 4 years ago
Labels: bug

#152 - Make subgraph c++

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

#151 - connected components mol_strategy

Pull Request - State: closed - Opened by aafshinfard over 4 years ago - 1 comment
Labels: enhancement

#150 - Gantt chart

Pull Request - State: closed - Opened by aafshinfard almost 5 years ago - 10 comments
Labels: enhancement

#149 - Physlr map c++

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 3 comments
Labels: Stale

#148 - Iterative mol sep 2

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

#147 - retrieve statistics for subgraphs of interest

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

#146 - sqcosbin and k3bin

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

#145 - port physlr split-minimizers to c++

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 2 comments

#144 - Arcs correction

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

#143 - Integration test fix

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: bug

#142 - Refactor physlr-map

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

#141 - physlr-make: update rules to reflect new features

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 7 comments

#140 - Change n to m

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: enhancement

#139 - physlr.py: remove unused code

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

#138 - Orient Bug Fix

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: bug

#137 - Check bed-to-path

Issue - State: open - Opened by jwcodee almost 5 years ago

#136 - Keep "BX_num" naming of molecules even after multiple rounds of molecule separation

Issue - State: closed - Opened by lcoombe almost 5 years ago - 1 comment
Labels: enhancement

#135 - No rule to make target

Issue - State: closed - Opened by stLFR almost 5 years ago - 3 comments

#134 - cossim (and kcliques) in progress

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

#133 - use std::max_element instead of manually updating maxVal

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: enhancement

#132 - variable `python_executable`

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

#131 - Use minimizers of each molecule rather than the barcode to map sequences

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

#130 - physlr: use ARCS to orient more pieces of the backbone

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

#129 - Physlr molecules C++ port

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 2 comments

#128 - Format for stLFR LinkedReads

Issue - State: closed - Opened by Ellis-Anderson almost 5 years ago - 3 comments
Labels: question

#127 - Metrics

Pull Request - State: closed - Opened by janetxinli almost 5 years ago

#126 - Add make into setup.py

Issue - State: open - Opened by jwcodee almost 5 years ago

#125 - Integration test

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: enhancement

#124 - change n to m

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

#123 - physlr-make: use k-mer repetitive threshold instead of 100

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 1 comment
Labels: enhancement

#122 - Makefile protocol variable

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

#121 - plotpaf.rmd: Sort query alphanumerically

Pull Request - State: closed - Opened by lcoombe almost 5 years ago

#120 - Add 2 hash generation to indexlr

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

#119 - Add chemistry option to physlr-make

Issue - State: closed - Opened by jwcodee almost 5 years ago - 1 comment

#118 - Makefile: add install rule

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 2 comments
Labels: enhancement

#117 - chainpaf hotfix

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: bug

#116 - Edge weight parameter 'm' -- fully rename from 'n'

Issue - State: closed - Opened by lcoombe almost 5 years ago - 1 comment

#115 - Float mapq values following paf chaining

Issue - State: closed - Opened by lcoombe almost 5 years ago - 2 comments
Labels: bug

#114 - plotpaf: permit float map values

Pull Request - State: closed - Opened by jwcodee almost 5 years ago - 2 comments
Labels: bug, invalid

#113 - Overlap unit test

Pull Request - State: closed - Opened by jwcodee almost 5 years ago
Labels: enhancement

#112 - Parallelize Overlap stage of physlr-overlap

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

#111 - No bridge pruning

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

#110 - Change Makefile to physlr-make

Pull Request - State: closed - Opened by jwcodee about 5 years ago - 2 comments
Labels: enhancement

#109 - Populate README

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

#108 - Permit float values in paf file

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

#107 - 0.2.0 Pipeline

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

#100 - physlr: improve path_to_fasta

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

#99 - Report junctions 2

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

#98 - Change pipeline

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

#97 - Makefile: add rule to differentiate %.qpos.paf.gz.pdf and %.paf.gz.pdf

Pull Request - State: closed - Opened by jwcodee about 5 years ago - 4 comments
Labels: bug

#96 - Report junctions

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

#95 - plotpaf.rmd: plot color and ideogram combined pdf

Pull Request - State: closed - Opened by jwcodee about 5 years ago - 8 comments
Labels: enhancement

#94 - Auto detect stLFR

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

#93 - Parse stLFR reads

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

#92 - Makefile: add parent directory to chainpaf rule

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

#91 - physlr.py: properly parse stlfr barcode

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