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4408407
add script to filter mashmap with tagged scaffolds
Delphine-L Jun 28, 2025
cbab71e
generate file with pairs and orientation
Delphine-L Jun 28, 2025
bc9d0d6
simplify the script and generate the sak for reversing
Delphine-L Jul 2, 2025
569682b
improve help
Delphine-L Jul 2, 2025
ce13035
remove hard paths and add argparser
Delphine-L Jul 2, 2025
2817798
improve arguments and help
Delphine-L Jul 2, 2025
22a4e19
improve arguments and help
Delphine-L Jul 2, 2025
187d12e
take file paths as inputs, and create directory if they don't exist
Delphine-L Jul 2, 2025
afd3a45
replace stout by log file
Delphine-L Jul 2, 2025
eeda5f1
fix help section
Delphine-L Jul 2, 2025
692c57a
now output hap2.vs.hap1.tsv file for ruby script
Delphine-L Jul 2, 2025
0a3b2cb
update the run all script with the new args for the scripts
Delphine-L Jul 2, 2025
c2c4a69
use the old pipeline without the micro tags
Delphine-L Jul 2, 2025
763139a
Merge branch 'galaxy_ready' into filter_mashmap
Delphine-L Jul 3, 2025
3f221a2
replace ruby script with renaming the fasta files to use gfastats
Delphine-L Jul 7, 2025
32e8644
fix bug with table separators
Delphine-L Jul 9, 2025
5ecce9e
fix renaming of agp columns that caused bug with unusual number of co…
Delphine-L Jul 15, 2025
457b2b6
fix issues caused by irregular column number
Delphine-L Jul 16, 2025
0120b05
Update dependencies and new usage
Delphine-L Jul 17, 2025
f482fbb
remove obsolete scripts
Delphine-L Jul 17, 2025
0f8bcaf
remove the reading fasta message
Delphine-L Jul 17, 2025
8dc6a04
now use hap1 and hap2 tags for pairing and takes the sex chromosome l…
Delphine-L Jul 17, 2025
1ed4514
improve logs, stop script if error, and add sex chromosome input
Delphine-L Jul 17, 2025
c9a11fd
update README with correct tags and command lines
Delphine-L Jul 17, 2025
4b26a0b
correct help text, got the sex chrom for birds wring
Delphine-L Jul 17, 2025
09b7f7e
update instruction on tagging sex chromosomes
Delphine-L Jul 17, 2025
6eeef67
add ouput and debugging
Delphine-L Jul 17, 2025
f5da7b2
improve logs
Delphine-L Jul 17, 2025
c8cb724
catch misssing arguments
Delphine-L Jul 22, 2025
2ceff30
add script to install dependencies
Delphine-L Jul 23, 2025
a68d554
add script to install dependencies
Delphine-L Jul 23, 2025
c7677b2
improve error reporting
Delphine-L Jul 24, 2025
a5bc0d6
fix issue with unloc renaming
Delphine-L Aug 5, 2025
a1f99de
Prepare for Packaging
Delphine-L Aug 6, 2025
4ca8608
Fix main functions
Delphine-L Aug 6, 2025
07c9c3b
improve documentation
Delphine-L Aug 7, 2025
d7375b9
improve documentation
Delphine-L Aug 7, 2025
b3260b2
Fix sex chromosome renaming
Delphine-L Aug 7, 2025
6b9d6c2
improve README
Delphine-L Aug 7, 2025
cdd67f4
add channel for conda installs
Delphine-L Aug 18, 2025
d370e42
correct typo in script name
Delphine-L Aug 18, 2025
b0a37fd
Merge AGPcorrect, hap_split, and unloc
Delphine-L Aug 19, 2025
765c2d6
update manuals
Delphine-L Aug 19, 2025
c7536b6
add error if pair missing in mashmap
Delphine-L Aug 20, 2025
025dd65
fix renaming for pairs absent from mashmap
Delphine-L Aug 20, 2025
2f5c69c
put functions inside the script instead of in separate file
Delphine-L Aug 21, 2025
c5207f8
fix typo
Delphine-L Aug 21, 2025
e345a22
fix issue for heterogametic assemblies, add error for duplicated scaf…
Delphine-L Aug 26, 2025
08c704f
fix some missing unloc renaming
Delphine-L Sep 3, 2025
bcd0733
skip renaming if not needed, and accelerate process with parrallel co…
Delphine-L Sep 3, 2025
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105 changes: 0 additions & 105 deletions AGPcorrect.py

This file was deleted.

9 changes: 9 additions & 0 deletions CHANGES.md
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# CHANGELOG


## v1.0 - 2025-08-06

- Initial Release



21 changes: 21 additions & 0 deletions LICENSE.txt
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MIT License

Copyright (c) 2025 Delphine Lariviere

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
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