MASON SIMULATOR
===============

MASON OPTIONS
-------------

VERBOSITY	VERBOSE

SEED	0
METHYLATION SEED	0
SEED SPACING	2048

FORCE SINGLE END	NO
NUM FRAGMENTS	1000

NUM THREADS	1
CHUNK SIZE	65536

METHYLATION FASTA IN	
OUTPUT FILE LEFT	simulator.left8.fq
OUTPUT FILE RIGHT	
PAIRED END SIMULATION	NO

MATERIALIZER OPTIONS
  VERBOSITY         	VERBOSE
  REFERENCE FASTA   	../input/random.fasta
  VARIANTS VCF      	

METHYLATION LEVELS OPTIONS
  VERBOSITY      	VERBOSE

  ENABLED	NO

  MEDIAN CG	0.6
  STDDEV CG	0.03
  MEDIAN CHG	0.08
  STDDEV CHG	0.008
  MEDIAN CHH	0.05
  STDDEV CHH	0.005

FRAGMENT SAMPLING
  SIZE MODEL     	NORMAL
  MIN SIZE       	100
  MAX SIZE       	400
  MEAN SIZE      	800
  STD DEV SIZE   	30

SEQUENCING
  SIMULATE QUALITIES 	YES
  SIMULATE MATE PAIRS	NO
  MATE ORIENTATION   	FORWARD-REVERSE (R1 --> <-- R2)
  SOURCE STRANDS     	BOTH
  SEQUENCING TECH    	ROCHE 454

BS-SEQ OPTIONS
  VERBOSITY      	NORMAL

  ENABLED	NO
  PROTOCOL	DIRECTIONAL
  CONVERSION RATE	0.99

ILLUMINA SEQUENCING
  READ LENGTH                  	100
  ERROR PROFILE FILE           	

  PROBABILITY INSERT           	5e-05
  PROBABILITY DELETE           	5e-05

  PROBABILITY MISMATCH SCALE   	1
  PROBABILITY MISMATCH AVG     	0.004
  PROBABILITY MISMATCH BEGIN   	0.002
  PROBABILITY MISMATCH END     	0.012
  MISMATCH RAISE POINT         	0.66

  MEAN QUALITY BEGIN           	40
  MEAN QUALITY END             	39.5
  STD DEV QUALITY BEGIN        	0.05
  STD DEV QUALITY END          	10

  MEAN MISMATCH QUALITY BEGIN  	40
  MEAN MISMATCH QUALITY END    	30
  STDDEV MISMATCH QUALITY BEGIN	3
  STDDEV MISMATCH QUALITY END  	15

  LEFT TEMPLATE FASTQ          	
  RIGHT TEMPLATE FASTQ         	

SANGER SEQUENCING
  UNIFORM READ LENGTH       	NO
  READ LENGTH MEAN          	400
  READ LENGTH ERROR         	40
  READ LENGTH MIN           	100
  READ LENGTH MAX           	200

  PROBABILITY MISMATCH BEGIN	0.005
  PROBABILITY MISMATCH END  	0.001
  PROBABILITY INSERT BEGIN  	0.0025
  PROBABILITY INSERT END    	0.005
  PROBABILITY DELETE BEGIN  	0.0025
  PROBABILITY DELETE END    	0.005

  QUALITY MATCH START MEAN  	40
  QUALITY MATCH END MEAN    	39.5
  QUALITY MATCH START STDDEV	0.1
  QUALITY MATCH END STDDEV  	2

  QUALITY ERROR START MEAN  	30
  QUALITY ERROR END MEAN    	20
  QUALITY ERROR START STDDEV	2
  QUALITY ERROR END STDDEV  	5

ROCHE 454 SEQUENCING
  READ LENGTH MODEL 	NORMAL
  MIN READ LENGTH   	10
  MAX READ LENGTH   	600
  MEAN READ LENGTH  	200
  STDDEV READ LENGTH	20

____INITIALIZING______________________________________________________________

Opening reference and variants file ... OK
Initializing fragment-to-contig distribution ... OK
Initializing simulation threads ... OK
Opening output file simulator.left8.fq ... OK
Opening output file simulator.out8.sam... OK

____READ SIMULATION___________________________________________________________

Distributing fragments to 2 contigs (1 haplotypes each) ... OK

Simulating Reads:
  1 (allele 1) .. (904 fragments) OK
  2 (allele 1) .. (96 fragments) OK
  Done simulating reads.

Joining temporary files ... OK
