Change the way chromosome length is calculated

[mfoll]

I just discovered that the size of chromosomes/contigs is written in the faidx index of the fasta reference file (see HTSlib). So my script to calculate that is useless (and very slow for nothing). I should rather simply use the faidx.

[mfoll]

This is creating the same header to put in the VCF as fasta2contigvcf.awk reference.fasta.fai but much faster (instantaneous instead of ~4min):

cat reference.fasta.fai | cut -f1,2 | sed -e 's/^/##contig=<ID=/' -e 's/\t/,length=/' -e 's/$/>/'

Note that '\t' doesn't work on Mac OS sed (see here), so use a real tab in the script.

[mfoll]

I also no longer need the less package in the Dockerfile.