Produce Sanger post-processing ready file names

[jgrg]

Add a Sanger specific command line option. It will select FASTA output. The --output argument must be <ToLID>.<#>.

Add a command line option to specify the number of curated assemblies.

With a Primary (None) assembly:

<ToLID>.1.primary.curated.fa 
<ToLID>.1.primary.chromosome.list.csv
<ToLID>.1.additional_haplotigs.curated.fa  # Sequence from "Haplotig" tagged scaffolds

With a Primary Hap1 assembly and an alternate Hap2 curated in a combined map:

<ToLID>.1.primary.curated.fa  # Sequence from "Hap1" tagged scaffolds)
<ToLID>.1.primary.chromosome.list.csv
<ToLID>.1.all_haplotigs.curated.fa  # Sequence from "Hap2" tagged scaffolds)

With two or more Hap... assemblies:

<ToLID>.hap1.1.primary.curated.fa 
<ToLID>.hap1.1.primary.chromosome.list.csv
<ToLID>.hap1.1.all_haplotigs.curated.fa  # Empty file

<ToLID>.hap2.1.primary.curated.fa 
<ToLID>.hap2.1.primary.chromosome.list.csv  # Empty if this was not a curated assembly
<ToLID>.hap2.1.all_haplotigs.curated.fa  # Empty file

# Repeated for Hap3 etc...

[additive3]

Assembly output options to be discussed but do not create random empty files

[additive3]

Ignore the creation of unused empty files.
Output scenarios:

Primary assembly + haplotigs fasta files

Hap1, Hap2, HapN fasta files

Hap1, Hap2, HapN fasta files (missing chrms from pairs) - Singleton metadata tag

Hap1 + all other seq fast files (eg multi haplotype assembly only Hap1 curated) - Primary metadata tag