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76bf22e3 · Merge branch '8-includeIsbpsMapping' into 'master' · Jan 04, 2024

Release: magatt-1.3

NEW: ISBPs anchoring on target genome is now included in the pipeline

ISBPs are provided as a BED file. Their sequences are extracted from the source genome with `bedtools getfasta` and then mapped on the target genome using `bwa mem`

v1.2

ed93ca70 · Merge branch 'missing_conda_rules' into 'master' · Jul 05, 2023

Major improvements:

- GMAP rescue on whole genome now run at the end of each chromosome batch. Major boost in execution time of the whole pipeline
- GMAP index: the indexing of the target with gmap_build has been removed. the index must be specified in the config.yaml file with `targetGmapIndex` (for -d option of gmapl) and `targetGmapIndexPath` (for -D option of gmapl)

Bugs: some bugs were corrected
 - reformatGmapWGGFF.py : bad initialisation of chromosomeMap dictionary
 - renameGffID.py: bad initialisation of chromosomeMap dictionary

v1.1

bc3fc1f7 · NEW single-isoform mode for transfert between disitant varieties · Sep 08, 2021
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Stable version 1.1: New single-isoform feature
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v1.0

587453ca · bug: if cds and mapping attributes existed in query GFF file, values were... · Dec 15, 2020
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First V1.0 of pipeline
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v0.3

fab0779b · new script to reformat output of gmap for whole genome results. Gmap create 1... · May 29, 2020

New version with Whole genome Gmap results integrated into the final GFF. CDS are also validated using fastavalidcds from exonerate

v0.2

178074c4 · add README.md · May 28, 2020
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Complete pipeline with README and How To
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v0.1

08268dae · 1st dev fial version · May 28, 2020
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v0.1 - First version of the full pipeline
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