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