add -a to bcftools concat

[glennhickey]

resolves #1808

[ASLeonard]

I might be getting lost in the maze of files, but maybe the files to be concat'ed are not actually indexed (i.e. the output of the merge+view step) despite most other VCFs being indexed.

cactus/src/cactus/refmap/cactus_graphmap_join.py

Lines 1472 to 1477 in 758003a

	cactus_call(parameters=['bgzip', header_path])
	cactus_call(parameters=['tabix', '-fp', 'vcf', header_path + '.gz'])
	updated_vcf_path = vcf_path + '.fix'
	cactus_call(parameters=[['bcftools', 'merge', vcf_path, header_path + '.gz'],
	['bcftools', 'view', '-S', all_sample_list_path, '-O', 'z']],
	outfile=updated_vcf_path)

Not sure how much .tbi versus .csi matters, but bcftools can index files on the fly in most commands with --write-index as a parameter (or -W and the choice of tbi/csi format in more recent versions), so could have fewer tabix calls and avoid non-indexed bgzip'ed files.