Compile cleanly without warnings with gcc 4.6.3
Fixed return status checks of fread calls
bcf_gt_type can now, optionally, give the index of the 2nd alt allele for GT_HET_AA genotypes
Merge pull request #33 from sm15/develop

bcf_gt_type can now, optionally, give the index of the 2nd alt allele
Merge branch 'develop' into bcftools+calling