refactoring, added graph-concordance subprogram
Add options so that the .sai file can be generated in a separate process.
change bam name parameter
do not load bwt if we aren't building sai
Merge branch 'master' of https://github.com/jts/sga
rewrite the variant index to use smaller records.

this is temporary and it should be rewritten to use tabix
Merge branch 'master' of https://github.com/jts/sga
optionally discard quality scores
minor output change
sga-variant-filters: use pipe instead of backtick
use bcftools in sga-variant-filters.pl
graph-concordance: do not abort when variants cannot be applied to haplotype
Merge branch 'master' of https://github.com/jts/sga