Modified to prevent ValueError for a certain vcf file

Solve the error, "Error in snpgdsVCF2GDS(vcf.file, gds.file, method = "biallelic.only", : unused argument (option = snpgds.option)", in the new version of SNPRelate.

Add new option '-r' to skip the step removing low quality data; Modify setup.sh for gdsfmt and SNPRelate packages no more supported by CRAN; Fix bugs

Add an option '-a' to determine the autosome number and '-A' to enable the multiple alignment process