Ecosyste.ms: Issues

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

GitHub / bcgsc/ntjoin issues and pull requests

#121 - Install conda using miniforge for macOS

Pull Request - State: closed - Opened by lcoombe about 2 months ago

#120 - Update README.md, azure-pipelines.yml

Pull Request - State: closed - Opened by lcoombe 2 months ago

#119 - Advice. Use only chromosomes as reference or the entire assembly?

Issue - State: closed - Opened by V-JJ 2 months ago - 2 comments
Labels: question

#118 - Add packaging dependency

Pull Request - State: closed - Opened by lcoombe 2 months ago

#117 - Error: No module named 'packaging'

Issue - State: closed - Opened by desmodus1984 2 months ago - 3 comments
Labels: stale

#116 - Suggestions on how to set up weights

Issue - State: closed - Opened by desmodus1984 2 months ago - 6 comments
Labels: stale

#115 - Overlap detection and edge weight

Issue - State: closed - Opened by tbusschau 3 months ago - 6 comments
Labels: question, stale

#114 - Prepare for release v1.1.5

Pull Request - State: closed - Opened by lcoombe 3 months ago

#113 - Fix for circular references

Pull Request - State: closed - Opened by lcoombe 3 months ago

#112 - File assemble / check_params does not exist

Issue - State: closed - Opened by Kaiden-exe 5 months ago - 5 comments

#111 - Invalid IUPAC characters

Issue - State: closed - Opened by Kaiden-exe 5 months ago - 3 comments

#110 - Update README.md

Pull Request - State: closed - Opened by lcoombe 6 months ago

#109 - Assertion error leading to deletion of scaffolds output file

Issue - State: closed - Opened by psal591 6 months ago - 13 comments

#108 - Installation failed / dependencies

Issue - State: closed - Opened by steinbrl 7 months ago - 6 comments
Labels: stale

#107 - High percentage of ambiguous bases.

Issue - State: closed - Opened by keith-harrison 8 months ago - 3 comments
Labels: question, stale

#106 - Merged chromosomes by telomere sequence?

Issue - State: closed - Opened by dirkjanvw 8 months ago - 7 comments

#105 - Prepare for release v1.1.4

Pull Request - State: closed - Opened by lcoombe 10 months ago

#104 - Update log message

Pull Request - State: closed - Opened by lcoombe 10 months ago

#103 - Large ntJoin refactor

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#102 - Use packaging module to compare semantic versions for pybedtools

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#101 - Prepare for release v1.1.3

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#100 - Bugfix for cases where there are no output paths, and overlap=True

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#99 - Prepare for release v1.1.2

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#98 - Fix for newer pybedtools versions

Pull Request - State: closed - Opened by lcoombe about 1 year ago

#96 - Update btllib dependency info

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

#95 - installation issue

Issue - State: closed - Opened by chunlinxiao almost 2 years ago - 7 comments
Labels: question

#94 - Mann-Kendall gives error with Numpy 1.24

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

#93 - Refactoring - pylint fixes

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

#92 - Viral contigs

Issue - State: closed - Opened by ohan-Bioinfo over 2 years ago - 4 comments
Labels: stale

#91 - Prepare for release v1.1.1

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

#90 - Remove packaged btllib, make it a dependency

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

#89 - Prepare for release v1.1.0

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

#88 - Unable to run ntJoin

Issue - State: closed - Opened by sunnyEV over 2 years ago - 2 comments
Labels: stale

#87 - Update btllib to v1.4.4

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

#86 - Add overlap feature

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

#85 - /ebio/abt3/nyoungblut/.zshenv:.:1: no such file or directory: /ebio/abt3/nyoungblut/.cargo/env

Issue - State: closed - Opened by nick-youngblut over 2 years ago - 7 comments
Labels: stale

#84 - I found a big problem in ntJoin script.

Issue - State: closed - Opened by Shokusei almost 3 years ago - 2 comments
Labels: question, stale

#81 - Add --len option to indexlr and update btllib

Pull Request - State: closed - Opened by vlad0x00 almost 3 years ago - 1 comment

#80 - CI fix

Pull Request - State: closed - Opened by lcoombe about 3 years ago

#79 - Prepare for release v1.0.8

Pull Request - State: closed - Opened by lcoombe about 3 years ago

#78 - Update btllib to 1.1.6

Pull Request - State: closed - Opened by vlad0x00 about 3 years ago - 1 comment

#77 - Update btllib

Pull Request - State: closed - Opened by vlad0x00 about 3 years ago - 1 comment

#76 - FileNotFoundError: [Errno 2] No such file or directory

Issue - State: closed - Opened by SuPrSh about 3 years ago - 3 comments
Labels: question

#75 - Code refactoring

Pull Request - State: closed - Opened by lcoombe about 3 years ago

#74 - Update btllib

Pull Request - State: closed - Opened by vlad0x00 about 3 years ago

#73 - Update azure-pipelines.yml

Pull Request - State: closed - Opened by lcoombe about 3 years ago

#72 - cat: standard output: No such file or directory

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

#71 - source file is in invalid format

Issue - State: closed - Opened by Steven-Kemp about 3 years ago - 5 comments
Labels: question

#70 - Translocation after scaffolding based on reference genome

Issue - State: closed - Opened by wuxingbo1986 over 3 years ago - 2 comments
Labels: stale

#69 - [2021-07-19 21:34:27] [ERROR] strain-13-plasmid.txt source file is in invalid format!

Issue - State: closed - Opened by ysawires12345678 over 3 years ago - 5 comments
Labels: question, stale

#68 - Prepare for release v1.0.7

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

#67 - Update indexlr

Pull Request - State: closed - Opened by vlad0x00 over 3 years ago - 1 comment

#66 - Update CI, stalebot

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

#65 - Error

Issue - State: closed - Opened by ibbaMI over 3 years ago - 2 comments

#64 - ntJoin:test error

Issue - State: closed - Opened by guanttttt over 3 years ago - 8 comments
Labels: question

#63 - Chromosome order after scaffolding

Issue - State: closed - Opened by NTNguyen13 over 3 years ago - 6 comments
Labels: question

#62 - Release v1.0.6

Pull Request - State: closed - Opened by lcoombe almost 4 years ago

#61 - Add optional parameter to use config file to specify reference(s)

Pull Request - State: closed - Opened by lcoombe almost 4 years ago

#60 - Set up paremeters

Issue - State: closed - Opened by AMMMachado almost 4 years ago - 4 comments
Labels: question, stale

#59 - Update azure-pipelines.yml

Pull Request - State: closed - Opened by lcoombe almost 4 years ago

#59 - Update azure-pipelines.yml

Pull Request - State: closed - Opened by lcoombe almost 4 years ago

#58 - No output after running

Issue - State: closed - Opened by NTNguyen13 almost 4 years ago - 9 comments
Labels: question

#57 - conda install the wrong package

Issue - State: closed - Opened by wuxingbo1986 almost 4 years ago - 1 comment
Labels: question

#56 - input multiple reference genome failed to parse

Issue - State: closed - Opened by yangyxt almost 4 years ago - 4 comments
Labels: stale

#55 - Input file Error

Issue - State: closed - Opened by ardy20 almost 4 years ago - 10 comments
Labels: stale

#54 - no changes in assembly

Issue - State: closed - Opened by jacorvar almost 4 years ago - 7 comments
Labels: stale

#53 - Release v1.0.5

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

#52 - Large scaffolds (parts of scaffolds) not assigned

Issue - State: closed - Opened by eriled about 4 years ago - 4 comments
Labels: stale

#51 - Fix compilation

Pull Request - State: closed - Opened by dpryan79 about 4 years ago - 1 comment

#50 - Update indexlr

Pull Request - State: closed - Opened by vlad0x00 about 4 years ago

#49 - Release v1.0.4

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

#48 - Time, warning fixes

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

#47 - Update indexlr

Pull Request - State: closed - Opened by vlad0x00 about 4 years ago - 4 comments

#46 - Error - reference.fa source file is in invalid format!

Issue - State: closed - Opened by eriled about 4 years ago - 5 comments
Labels: question

#45 - Conda install fails

Issue - State: closed - Opened by rungitta about 4 years ago - 1 comment
Labels: question

#44 - Conda install fails

Issue - State: closed - Opened by rungitta about 4 years ago - 3 comments
Labels: documentation

#43 - Add verbose option to indexlr

Pull Request - State: closed - Opened by vlad0x00 about 4 years ago

#42 - Fix indexlr for clang

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

#41 - Fix for new pylint version

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

#40 - btllib port of indexlr

Pull Request - State: closed - Opened by vlad0x00 about 4 years ago - 4 comments

#39 - ntJoin command time -v -o

Issue - State: closed - Opened by azrasid about 4 years ago - 9 comments
Labels: question

#38 - time: command not found... Error 127

Issue - State: closed - Opened by sadikmu over 4 years ago - 2 comments
Labels: stale

#37 - Problem with multiple references

Issue - State: closed - Opened by matt-shenton over 4 years ago - 16 comments

#36 - Add --id and --bx options

Pull Request - State: closed - Opened by vlad0x00 over 4 years ago - 1 comment

#35 - Fix for edge cases that could duplicate sequence

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

#34 - Increased assembly size

Issue - State: closed - Opened by elsemikk over 4 years ago - 4 comments
Labels: stale

#33 - failure to install from git

Issue - State: closed - Opened by drashwinelkar over 4 years ago - 3 comments

#32 - make error using a container for ntJoin

Issue - State: closed - Opened by drashwinelkar over 4 years ago - 4 comments
Labels: stale

#31 - Implement max gap size parameter

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

#30 - Strip terminal gap sequence from unassigned scaffolds

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

#29 - ntjoin_assemble.py: Bugfix to linear path function

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

#28 - Adding sequence from the reference into gaps

Issue - State: closed - Opened by olekto over 4 years ago - 6 comments
Labels: enhancement, stale

#27 - malformed bed entry?

Issue - State: closed - Opened by cistarsa over 4 years ago - 5 comments
Labels: documentation, question

#26 - Make bf query slightly faster

Pull Request - State: closed - Opened by vlad0x00 over 4 years ago - 1 comment

#25 - No cut option

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

#24 - How will ntJoin handle gaps with Ns in a scaffold?

Issue - State: closed - Opened by rajewski over 4 years ago - 2 comments
Labels: question

#23 - Output same as input

Issue - State: closed - Opened by ViriatoII almost 5 years ago - 8 comments

#22 - Make error after successful instalation

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

#21 - ntJoin: Update to handle fasta files with any extension

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