Pull additional metadata as header file

[priyanka-surana]

Description of feature

Include additional metadata in aligned file headers. Requested by Shane.

I would like/expect some additional information in the @SQ headers, especially if these are to go to the ENA.

• SP (species)
• AS (assembly identifier) - the GCA accession
• AN (alternate name) - the chromosome names that have been assigned, so that we can see, for example, which chromosomes are X/Y/W/Z/MT etc. I would argue that these should be the primary names and the INSDC accessions the alternates, but that would probably have to be discussed.
• I would also suggest pointing to the NCBI version of the assembly in the UR tag rather than a location on Sanger disk - unreadable outside of Sanger and exposes our directory structure to the outside.

[tkchafin]

Posting link for reference on expected BAM header fields for ENA submission

@HD	VN:1.4	GO:none	SO:coordinate
@SQ	SN:2L	LN:49364325	UR:http://www.vectorbase.org/content/anopheles-gamb
iae-pestchromosomesagamp3fagz	AS:AgamP3	M5:a4da4bafa82830c0a418c5a42138377b
	SP:Anopheles gambiae