fix warning "Use of uninitialized value in subroutine entry"
setting to 0 as per POD and Leo's request
always write the sequence to the current seqio - fix for creating lots of empty output files
fix warning "Use of uninitialized value in subroutine entry"

PR #5
Pulling in Roy's bug-fixes

- always write the sequence to the current seqio - fix for creating lots of empty output files
- fix warning "Use of uninitialized value in subroutine entry"