cerebis/bin3c issues and pull requests

#41 - update requirements.txt to work for python2

Pull Request - State: open - Opened by hyphaltip almost 2 years ago

#40 - Check that HD record exists or place in try/catch block

Issue - State: open - Opened by cerebis almost 3 years ago
Labels: bug

#39 - One huge cluster

Issue - State: open - Opened by orctyr about 3 years ago - 8 comments

#38 - What is the `--tip-size` used for?

Issue - State: open - Opened by ruoyu1123 over 3 years ago - 1 comment

#37 - binning with references splitted into fragments

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

#36 - Bump pyyaml from 3.13 to 5.4

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#35 - docker image failure in singularity

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

#34 - Switch to HDF5 based storage of intermediate data types.

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#34 - Switch to HDF5 based storage of intermediate data types.

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#33 - Check what how supplied BAM files were made.

Issue - State: open - Opened by cerebis over 4 years ago
Labels: enhancement

#32 - Memory Error while running in VirtualBox

Issue - State: open - Opened by cerebis almost 5 years ago - 1 comment
Labels: Analysis problem

#31 - Building Infomap Error

Issue - State: closed - Opened by davidcalfran almost 5 years ago - 2 comments

#30 - Building on OSX requires GCC

Issue - State: closed - Opened by cerebis almost 5 years ago - 1 comment
Labels: Installation

#29 - Installation through pip requires newer pip version

Issue - State: open - Opened by cerebis almost 5 years ago - 1 comment
Labels: Installation

#28 - Modifying experimental details post-map creation

Issue - State: open - Opened by cerebis over 5 years ago
Labels: enhancement

#27 - Extract could operate on either type of BAM ordering

Issue - State: open - Opened by cerebis over 5 years ago
Labels: enhancement

#26 - Extracting BAM on combined contact maps not supported

Issue - State: open - Opened by cerebis over 5 years ago
Labels: bug, low priority

#25 - Merge updates from megahit branch to pgtk

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

#24 - resolves #23

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

#23 - Method assumes a cigar string will exist

Issue - State: closed - Opened by cerebis over 5 years ago - 1 comment
Labels: bug

#22 - Check for the existence of all required files immediately.

Issue - State: open - Opened by cerebis over 5 years ago
Labels: enhancement

#21 - Emphasise read cleanup in documentation

Issue - State: open - Opened by cerebis over 5 years ago
Labels: enhancement

#20 - Help for sub-commands not printing when -h invoked

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

#19 - Bad use of empty list in cluster_report when no-spades=True

Issue - State: closed - Opened by cerebis over 5 years ago
Labels: bug

#18 - Consider adding runtime problem introspection and guidance

Issue - State: open - Opened by cerebis over 5 years ago
Labels: enhancement

#17 - Likely "out of memory" exception when analysing a large problem space.

Issue - State: closed - Opened by orctyr over 5 years ago - 18 comments
Labels: Analysis problem

#16 - Switch to storing contact map as hd5

Issue - State: closed - Opened by cerebis over 5 years ago - 1 comment
Labels: enhancement

#15 - centos6 image still seems to have "kernel too old"

Issue - State: closed - Opened by cerebis over 5 years ago - 1 comment

#14 - Create a Docker and Singularity image

Issue - State: closed - Opened by cerebis almost 6 years ago

#12 - update readme on pgtk thread

Issue - State: closed - Opened by cerebis almost 6 years ago

#11 - Resolving yaml.load vulnerability

Pull Request - State: closed - Opened by cerebis about 6 years ago

#10 - Pickling ContactMap

Issue - State: closed - Opened by cerebis over 7 years ago

#9 - Poor time complexity of some algorithm choices

Issue - State: closed - Opened by cerebis over 7 years ago - 2 comments
Labels: low priority

#8 - Target FASTA path can become stale if files moved

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#7 - Consider full workflow UX command

Issue - State: open - Opened by cerebis over 6 years ago

#6 - Default arguments in clustering override those used in map creation

Issue - State: closed - Opened by cerebis over 6 years ago

#5 - Print command line to log

Issue - State: closed - Opened by cerebis over 6 years ago

#4 - Relative paths when running stages

Issue - State: open - Opened by cerebis over 6 years ago

#3 - [AD] cosmetics

Pull Request - State: closed - Opened by koadman over 6 years ago

#2 - Coverage outlier identification

Issue - State: closed - Opened by cerebis over 6 years ago - 1 comment
Labels: wontfix

#1 - Coverage analysis for any assembler type

Issue - State: closed - Opened by cerebis over 6 years ago - 2 comments

GitHub / cerebis/bin3c issues and pull requests