NAME

Prefs

SYNOPSIS

    require Prefs;
    my %User_Preferences = %Prefs::User_Preferences;

DESCRIPTION

This is the configuration module for TURNIP. Preferences are supplied via .conf files in the conf directory of the TURNIP software distribution.

FEEDBACK

Reporting Bugs

Please report bugs to the author.

AUTHOR

Rob Davey

APPENDIX

Here is the conf/example.conf file for posterity:

##level of TURNIP output
verbose=1

## debug
debug=0

##base data path directory
datapath=../../data/cerevisiae/

##write temporary ascription files to disk at each position.
##for machines with large RAM (1-2Gb or more), this should be set to 0
##for those with lower RAM (<=1Gb), this should be set to 1
##NB - this may be beneficial on all machines if using very fast disks/solid state drives
write_temp_ascrib=0

##file suffix of your quality score files
qual_db_suffix=_qual.clipped.sc

##file suffix of your fasta files
fasta_db_suffix=_fasta.clipped.sc

##use the muscle multialignments for gapped reads
use_multialignments_mode=1

##ignore positional ascriptions whereby the subject and query alignments are the same
##default 1 should be faster than 0, where identical alignments are still recorded and
##outputted
omit_identical_positional_alignments=1

##simulate differing read coverage
simulate_read_coverage=0

##take a fraction of existing reads to simulate differing read coverage (percentages as values from 0.0 - 1.0)
coverage_modifier=0.5

##constrain the analysis to a region of a given consensus using slicemin and slicemax as bounds
constrain_to_region=0

##min bound for constraint (inclusive)
slicemin=4080

##max bound for constraint (inclusive)
slicemax=4180

##write backup copies of output files
write_backups=0

##write output files using nstore to ensure compatability between 64bit and 32bit Storable implementations
write_nstore_dat_files=1

##use multi-processor acrhitectures
smp=1

##if smp, then how many processes/cores to use
processes=4

##filter out polymorphisms with read counts <= max_mismatch_threshold
max_mismatch_threshold=1

##
short_length = 20

##
buffer = 40

##
allowed_mismatches = 50

##
allowed_shortness = 38

##
min_qual = 38

##
min_reinforcing_required = 2

##
min_good = 10

##
flanks_buffer = 20

##strain list
strains=273614X,322134S,378604X,BC187,DBVPG1106,DBVPG6040,K11,NCYC110,NCYC362,
S288c,ScDB53,ScDB65,ScDB73,ScDB88,Sp1374,SpDB44,SK1,UW03_461_4,UW05_227_2,
UW05_217_3,W303,Y9,Y12,Y55,YIIc17_E5,YJM975,YJM978,YJM981,YPS128,YPS606,YS4,YS9,UW87_2421

The rest of the documentation details each of the object methods. Internal (private) functions are preceded by an underscore (_)