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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`

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

Stable version 1.1: New single-isoform feature

First V1.0 of pipeline

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

Complete pipeline with README and How To

v0.1 - First version of the full pipeline