Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / VirologyCharite/sars2seq issues and pull requests
#34 - Generalize to no longer be SARS-CoV-2 specific
Pull Request -
State: open - Opened by terrycojones over 2 years ago
- 1 comment
#33 - Added typing hints and switched to using black for formatting
Pull Request -
State: closed - Opened by terrycojones over 2 years ago
#32 - Use black
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#31 - Renamed SARS2Genome to SARS2Alignment
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#30 - Updated README docs.
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
- 1 comment
#29 - Added being able to tell the edlib aligner to respect ambiguous nucleotide codes
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#28 - Added some README docs, a coverage function, and a helper function for examining sites in multiple genomes.
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#27 - Added support for the dark-matter edlib aligner.
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
- 1 comment
#26 - Added 'aaOffset' (in the reference and the genome) to info returned by offsetInfo, and changed 'offset' to 'ntOffset'
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#25 - Add script, library code, and tests for getting information about genome sites
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#24 - Tiny changes
Pull Request -
State: closed - Opened by terrycojones almost 3 years ago
#23 - Added summarizeNoCoverage flag (defaults to False) to getSubstitutionsString
Pull Request -
State: closed - Opened by terrycojones about 3 years ago
- 1 comment
#22 - Added tests to show the problem described in https://github.com/VirologyCharite/sars2seq/issues/21
Pull Request -
State: closed - Opened by terrycojones about 3 years ago
#21 - getSubstitutionsString doesn't report no coverage at position with X
Issue -
State: open - Opened by terrycojones about 3 years ago
#20 - Preliminary testing of getSubstitutionsString
Pull Request -
State: closed - Opened by terrycojones about 3 years ago
- 1 comment
#19 - Added additional known insertions
Pull Request -
State: closed - Opened by bamueh about 3 years ago
- 1 comment
#18 - Added improved error message and updated insertions
Pull Request -
State: closed - Opened by bamueh about 3 years ago
#17 - Small changes to translate.py
Pull Request -
State: closed - Opened by bamueh over 3 years ago
- 2 comments
#16 - Spike insertion additions
Pull Request -
State: closed - Opened by bamueh over 3 years ago
- 1 comment
#15 - Added better error checking and function to look for known Spike insertions
Pull Request -
State: closed - Opened by bamueh over 3 years ago
#14 - Remove insertion check for Spike
Pull Request -
State: closed - Opened by bamueh over 3 years ago
#13 - Allow insertions into the reference for the Spike
Issue -
State: closed - Opened by bamueh over 3 years ago
- 1 comment
#12 - Added code that correctly aligns Spike sequences
Pull Request -
State: closed - Opened by bamueh over 3 years ago
#11 - Fix spike gap alignments
Issue -
State: closed - Opened by bamueh over 3 years ago
#10 - Fixed slippery sequence -1 frameshift translation.
Pull Request -
State: closed - Opened by terrycojones over 3 years ago
#9 - Incorrect deletion flagged in aa in ORF1ab with B.1.617 sequence
Issue -
State: closed - Opened by terrycojones over 3 years ago
#8 - Small improvements to describe-genome.py to better handle errors and report variant tests that fail
Pull Request -
State: closed - Opened by terrycojones almost 4 years ago
#7 - Fixed a few instances of incorrect ordering of variables.
Pull Request -
State: closed - Opened by terrycojones almost 4 years ago
- 1 comment
#6 - Swap between reference and sequence to analyse
Issue -
State: closed - Opened by bamueh almost 4 years ago
- 1 comment
#5 - Allow passing an already-made alignment to SARS2Genome
Pull Request -
State: closed - Opened by terrycojones almost 4 years ago
#4 - AttributeError: 'Features' object has no attribute 'featuresDict'
Issue -
State: closed - Opened by bamueh almost 4 years ago
Labels: bug
#3 - Major code rearrangement / simplification to just do one alignment for the whole genome.
Pull Request -
State: closed - Opened by terrycojones almost 4 years ago
#2 - Fixes #1
Pull Request -
State: closed - Opened by UdoGi about 4 years ago
- 2 comments
#1 - The __and__ and __or__functions in checker.py should return a copy of self
Issue -
State: closed - Opened by terrycojones about 4 years ago