I installed bwa-0.6.1 and index human genome like
bwa index -a bwtsw hg19.fa
it generate five files (.amb, .ann, .bwt, .pac, .sa files) but with bwa-0.5.9 there are nine index files (.fai, .rpac, .amb, .ann, .pac, .bwt, .rbwt, .rsa, .sa nine files)
did I miss something in options of bwa index? What should I do to make it right?
Thanks a lot