Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Flagtastrophe #290

Merged
merged 96 commits into from
Nov 8, 2024
Merged

Flagtastrophe #290

merged 96 commits into from
Nov 8, 2024

Conversation

ekg
Copy link
Collaborator

@ekg ekg commented Nov 1, 2024

This implements a major rewrite of the command line interface to remove lots of rarely used options and focus on commonly used ones and clear documentation of them.

ekg added 30 commits November 1, 2024 11:11
@ekg
fix: Update CLI interface for wfmash
25a06b0
@ekg
fix: feat: Add missing variable declarations and remove duplicate opt…
49ac285 
…ion declarations in parse_args.hpp
@ekg
feat: remove duplicate no_merge flag declaration in parse_args.hpp
1948c6b
@ekg
fix: remove duplicate approx_mapping flag and declare kmer_size
de74a57
@ekg
fix: Add approx_mapping flag to parse_args.hpp
8135f96
@ekg
fix: change short option for approx_mapping to -m
2b19ea5
@ekg
feat: Add short option -k for kmer-size and -w for sketch-size
b94feca
@ekg
Here is the one-line commit message based on the provided diffs:
f4586b3 
chore: remove unused WFA/WFlign options from parse_args.hpp
@ekg
feat: add num_mappings_for_short_seq, lower_triangular, and skip_self…
b22faa7 
… flags
@ekg
fix: Remove unused CLI arguments and set default values directly
4e48999
@ekg
fix: Fix SEARCH/REPLACE block to exactly match src/interface/parse_ar…
9a32fbd 
…gs.hpp
@ekg
feat: change short option for --one-to-one from -4 to -o
86948d7
@ekg
fix: remove drop-low-id parameter
e43ac7d
@ekg
feat: add default parameter for keep_low_pct_id
2a1b69e
@ekg
fix: Update help text formatting
4942f70
@ekg
feat: Reorganize help text in parse_args.hpp
20ae047
@ekg
fix: Add missing options_group to argument parser
34be435
@ekg
feat: Add improved argument parser formatting
d2ae928
@ekg
fix: remove invalid usageindent parameter from parse_args.hpp
0cf4dc5
@ekg
feat: Add version and help flags to system options group
842fda1
@ekg
feat: Remove unnecessary indentation from wfmash help output
69a1d24
@ekg
feat: Adjust help text formatting to match minimap2's style
17cd72a
@ekg
fix: remove duplicate "Options:" header
40bc949
@ekg
feat: Improve help text conciseness
904cd04
@ekg
fix: remove extra "wfmash" line from help output
9d314ec
@ekg
feat: Add lower triangular option to mapping parameters
99b7574
@ekg
feat: compress query prefix option text
cb189e4
@ekg
fix: Update default group prefix and help text
d697002
@ekg
feat: add default group prefix character to help text
944d984
@ekg
feat: use shorter param name for WFA scoring
4a876b8
@AndreaGuarracino
Copy link
Member

Update the README accordingly to all the new changes. For example, in the example we should not show -s 20k when we align sequences, while we should show an example where users can specify high -s/-P values if they use -m.

ekg added 27 commits November 5, 2024 14:34
@ekg
feat: Update README to reflect current MashMap 3.5 and WFA usage
2cb57a5
@ekg
feat: Update README with concise and clear description
7a30e28
@ekg
feat: Add explanation for mapping length limits in README
89421e4
@ekg
feat: Add length of target subsets in base pairs to output
de3eb79
@ekg
fix: add debug output to track sequence size metrics
3406ccd
@ekg
build: Fix compilation error in parse_args.hpp
8ced912
@ekg
fix: Update reference size calculation in parse_args.hpp
de71486
@ekg
chore: comment out debugging output in parse_args.hpp
7f7c015
@ekg
feat: Add target sequence information to log output
4ee3d60
@ekg
fix: Move logging information before mapping indexing
db6ffac
@ekg
feat: Add logging of target sequence information before indexing
7609573
@ekg
unaider
057a033
@ekg
feat: Compute and display query and target lengths separately
80f1d0d
@ekg
fix: initialize sequence names before calculating lengths
49f5182
@ekg
feat: Move sequence length reporting to after sequence manager initia…
3c3d9f8 
…lization
@ekg
build: Initialize sequence names and calculate lengths in constructor
6bd8b4c
@ekg
build: Improve output conciseness and remove duplicate line
9b56f32
@ekg
fix: Replace "seqs" with "queries" in output messages
a95273c
@ekg
chore: remove detailed statistics line
5e2e245
@ekg
fix: Set default group prefix delimiter to '#'
e9f0b07
@ekg
fix: Remove warning about single file all-vs-all mapping
0ccae8d
@ekg
fix: Set default group prefix delimiter to '#' and enable prefix skip…
804cbde 
…ping
@ekg
feat: add group information to query and target count output
c14658f
@ekg
refactor: split long log message into multiple lines
23bb4c0
@ekg
fix: Add check for .fai index files before parameter validation
dedb843
@ekg
Revert "fix: Add check for .fai index files before parameter validation"
3653365 
This reverts commit dedb843.
@ekg
feat: Add parallel index building to improve performance
0e123bd
@ekg ekg merged commit c8985d3 into main Nov 8, 2024
1 check passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@ekg @AndreaGuarracino @ASLeonard