Add hts_set_fai_filename(); parse .fai in sam_hdr_read()

Provide hts_set_fai_filename() to (optionally) set htsFile::fn_aux
instead of from a third hts_open() parameter.  Implement deriving @SQ
headers from the .fai file if necessary, much as vcf_hdr_read() does.
Remove now-unused fn_aux hts_open() parameter

(Only test/test_view.c passed non-NULL here, but it was passing a .fa
filename rather than .fa.fai, so it should have been passing NULL too.)
Reinstate distinct bgzf_check_EOF() status for seek failure

In bam_hdr_read(), report errors from bgzf_check_EOF() regardless of
hts_verbose, especially because after seeking the stream is likely in
an invalid state for reading the header.

Fixes samtools/samtools#18.
bcf_gt_type can now, optionally, give the index of the 2nd alt allele for GT_HET_AA genotypes