simplify variables
removes some redundant checks
simplifies condition
more use of FVC
further simplifications
removes further needless checks
updates citation
minor cleanup
Revert "more use of FVC"

This reverts commit 71218a5da1b1540165ac7081edc130d9201ceaf2.
Merge branch 'microopt'
updates kseq.h
more micro optimizations
Merge branch 'master' into coverage