Skeleton of ivr-typer.pl. So far it only takes reads from a samtools command pipeline and converts them to fasta for use with BLAT
Allow only part of pipeline to be run i.e. resumed. Less stringent on lane names
Merge branch 'testing'

Conflicts:
	assembly_scripts/assembly_pipeline/batch_assemble.pl
Merge in skeleton ivr typer (doesn't do much yet) and some assembly pipeline
improvements.