update script modified by kentnf
copy virus_detect.pl
put file or correct position
correct path and folder
finish the structure of alignAndCorrect
update the pileup_to_contig
the remove redundancy also use the preivous code, need update later
finish all except remove redundancy
fix bugs before remove redundancy
almost finish remove redundancy as subroutine except base correction
finish all subroutine, start debuging
fix bug: peform remove redundancy on assembly and combined contigs
fix bug: base correction
fix bug: remove redundancy for assembled contigs
fix bug: should keep contig file after base correction
fix bug: all running bugs are fixed, next for comparison with prev version
fix bugs: filter_SAM
bug fixed: generate pre.pileup
bug fixed: align with multiple hits
bug fixed: extractConsensus java to perl for aligned contigs