SeqCons
=======

__OPTIONS____________________________________________________________________

VERBOSITY              	NORMAL
OPERATION              	contig-wise MSA + consensus

INPUT FILE             	alns1.sam
OUTPUT READS           	alns1.contig_consensus.sam
OUTPUT CONSENSUS       	alns1.contig_consensus.fa

OVERLAP MIN LENGTH     	20
OVERLAP MAX ERR-RATE   	5
OVERLAP MIN COUNT      	3
OVERLAP WINDOW SIZE    	20

K-MER SIZE             	20
K-MER MAX OCCURRENCES  	200

REALIGNMENT BANDWIDTH  	10
REALIGNMENT ENVIRONMENT	20

__LOADING DATA_______________________________________________________________

  Loading alignments from alns1.sam...OK

__COMPUTATION________________________________________________________________

Performing consensus computation... OK
Performing realignment... OK

__WRITING RESULT_____________________________________________________________

Writing consensus to alns1.contig_consensus.fa ... OK
Writing alignments to alns1.contig_consensus.sam ... OK

Overall time: 1.00215 s

Done.  Have a nice day.
