MGP v8 annotations and GRCm39

v0.6.0 - GRCm39 genome build and new Docs

• Restructured the documentation, using mkdocs. The new User Guide lives at this address: http://felixkrueger.github.io/SNPsplit/

• Reworked all of SNPsplit to reflect changes of the Mouse Genomes Project. This includes the overdue switch-over to the latest v8 annotation (available here) and the GRCm39 mouse genome build

• Kept the old v5 (and v7) genome build instructions as legacy documentation

SNPsplit

• Added an option --single_end to skip the paired-end auto-detection entirely (which failed for e.g. alignments with STAR see here)

SNPsplit_genome_preparation

• Changed the chromosome detection regex to a non-greedy match (so it only uses the NAME entry following the ID=NAME, up to, but not including the first ,)