Ecosyste.ms: Issues

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GitHub / KatyBrown/CIAlign issues and pull requests

#71 - CIAlign vs HmmCleaner, PREQUAL, and spruceup

Issue - State: open - Opened by fdecarpentier 2 months ago

#70 - Fix AttributeError in drawMarkUp by converting nams to a list

Pull Request - State: open - Opened by dprokopov 2 months ago

#69 - minor bug - no error if the consensus type specified doesn't exist

Issue - State: open - Opened by KatyBrown 2 months ago
Labels: bug, to do

#68 - added option to keep sequence names in mini alignments

Pull Request - State: open - Opened by KatyBrown 6 months ago

#67 - Option for original sequence names in plots

Issue - State: closed - Opened by PeterP-GH 6 months ago - 1 comment

#66 - additional stats plots and mini alignment options

Pull Request - State: closed - Opened by KatyBrown 8 months ago

#65 - added function residueChangeCount in consensusSeq

Pull Request - State: closed - Opened by Jebthesheep101 8 months ago - 1 comment

#64 - finished function for plotting residue frequencies

Pull Request - State: closed - Opened by KatyBrown 8 months ago

#63 - Bar graph function with documentation

Pull Request - State: closed - Opened by Jebthesheep101 8 months ago

#62 - Update consensusSeq.py

Pull Request - State: closed - Opened by Jebthesheep101 8 months ago

#61 - updated help function plot_consensus_identity

Pull Request - State: closed - Opened by Jebthesheep101 8 months ago

#60 - added documentation for the function in consensusSeq

Pull Request - State: closed - Opened by Jebthesheep101 8 months ago

#58 - modules not found upon installation

Issue - State: closed - Opened by jonathan-wells 11 months ago - 3 comments

#57 - Update README and fix markup bug

Pull Request - State: closed - Opened by schnamo 11 months ago

#56 - Allow CIAlign to handle gunzipped fasta files.

Issue - State: open - Opened by Thernn88 over 1 year ago
Labels: enhancement

#55 - how to get row labels labeled in output SVG image?

Issue - State: closed - Opened by hhg7 over 1 year ago - 1 comment

#54 - Update conda CIAlign to latest version?

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

#53 - Alignment cropping only outputs log file, but no alignment file

Issue - State: open - Opened by ahaegeman over 1 year ago
Labels: to do

#52 - Missing modules with installation

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

#51 - alternative colours

Issue - State: open - Opened by KatyBrown over 1 year ago - 2 comments
Labels: enhancement

#50 - Remove columns with user-defined percentage missing value

Issue - State: open - Opened by Phismil almost 2 years ago - 1 comment
Labels: enhancement

#49 - File naming for the output

Issue - State: open - Opened by dgslos almost 2 years ago - 2 comments
Labels: enhancement

#48 - IndexError: tuple index out of range

Issue - State: closed - Opened by dgslos about 2 years ago - 3 comments
Labels: bug

#47 - Multiple changes for release of version 1.1.0

Pull Request - State: closed - Opened by KatyBrown about 2 years ago

#46 - Crop divergent

Pull Request - State: closed - Opened by KatyBrown about 2 years ago

#45 - Retain sequences

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

#44 - Bump numpy from 1.21.0 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#43 - More cleaning/filtration steps

Issue - State: open - Opened by fanninpm over 2 years ago - 1 comment
Labels: enhancement

#42 - Bump numpy from 1.19.5 to 1.21.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#41 - Add paper to readme.md

Pull Request - State: closed - Opened by schnamo almost 3 years ago

#40 - Let the user change the '--remove_insertions' percentage

Issue - State: closed - Opened by lukaszsobala almost 3 years ago - 2 comments
Labels: added

#39 - Ci testing

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

#38 - CI testing

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

#37 - Updated cmt tables

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

#36 - QuanTest2, time and memory tables, unit test updates, minor adjustments

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

#35 - Generating a Consensus Sequence like Geneious with Threshold

Issue - State: open - Opened by bigben446 over 3 years ago - 1 comment
Labels: enhancement

#34 - temp fix for ranges

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

#33 - Added more parameter

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

#32 - minor edits for benchmarking and to mini alignment colours

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

#31 - tiny adjustments

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

#29 - parameter min and max values

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

#28 - keep_gaponly?

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

#27 - merge the benchmarking branch into master

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

#26 - unit tests

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

#24 - first unit tests and bug fix in crop ends

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

#23 - measure time and memory utility function

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

#22 - CIAlign influences aligment itself

Issue - State: closed - Opened by dgslos almost 4 years ago - 3 comments
Labels: solved

#21 - Update .gitignore

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

#20 - The sequences in your alignment are not all the same length

Issue - State: closed - Opened by majie5976 about 4 years ago - 2 comments
Labels: solved

#19 - memory usage

Issue - State: closed - Opened by blahah about 4 years ago - 3 comments
Labels: to do

#18 - Multithreading support

Issue - State: open - Opened by dgslos about 4 years ago - 1 comment
Labels: enhancement

#17 - Cleaning up very large insertions

Issue - State: closed - Opened by dnieuw over 4 years ago - 2 comments
Labels: to do

#16 - Bioconda

Issue - State: closed - Opened by geboro over 4 years ago - 3 comments
Labels: enhancement, added

#15 - CIAlign installed by pip3 returned an error that 'no module name _version'

Issue - State: closed - Opened by keaimajia over 4 years ago - 3 comments
Labels: fixed

#14 - minor error handling added

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

#13 - getAAColours function lacks the color of amino acid 'B'

Issue - State: closed - Opened by keaimajia over 4 years ago - 1 comment
Labels: fixed

#12 - Benchmarking devel

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

#11 - Replacing Us with Ts

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

#10 - Debugging katy

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

#9 - added version to manual and replaced remaining runtime errors with cl…

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

#7 - No --version option

Issue - State: closed - Opened by tseemann over 4 years ago - 1 comment
Labels: fixed

#6 - Backtrace output instead of clean error messages?

Issue - State: closed - Opened by tseemann over 4 years ago - 1 comment
Labels: fixed

#5 - bug fixes for next release

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

#4 - Docs devel

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

#3 - added consensus to main script

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

#2 - removed dictionary requirement

Pull Request - State: closed - Opened by KatyBrown almost 6 years ago

#1 - added cropping functions to main script

Pull Request - State: closed - Opened by KatyBrown almost 6 years ago