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config_file.txt
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#####################################################
### CONFIG FILE FOR BARCODE_BINNER
#####################################################
##this file contains key configuration information
##a config file is used for consistency given the program
##may be restarted multiple times with multiple users
##thus an expert user is allowed to fully control how it setsup
## and other users can simply execute the program
##unlike other config files variable names are case sensitive
#white space is a delimiter and thus adhored within a key or a value
#NOTE -- white space will be removed between keys and values
###############################################################
#NOTE -- leading white space on a line associates the data on
# next line with previous line (don't do it)
###############################################################
[BINS]
#bins/bags are where samples will be placed
#BADBARCODE is where barcodes go that don't match a sample barcode
#FAILEDBIN is the bin/bag where all bins go if they don't mactch provide
#regex: is used for regular expression denotation
c_A11 = gha_c_A11
c_A12 = gha_c_A12
c_A13 = gha_c_A13
c_A14 = gha_c_A14
c_C01 = gha_c_C01
c_C02 = gha_c_C02
c_P22 = gha_c_P22
i_A11 = gha_i_A11
i_A12 = gha_i_A12
i_A13 = gha_i_A13
i_A14 = gha_i_A14
i_C01 = gha_i_C01
i_C02 = gha_i_C02
i_P22 = gha_i_P22
i_V31 = gha_i_V31
i_V32 = gha_i_V32
M42 = gha_M42
GHANA = regex:gab_
MALAWI = regex:mal_
[REQUIRED]
FILEOUTSAMPLE=outputfile_samples_processed.tsv
# is where data from input is saved once scanned
FILEOUTBAD=outputfile_badcodes.tsv
# all BADCODE designations
# essentially everything that can't match as sample
# barcodes that don't match pattern or don't map to sample
BAGSIZE=50
# default size (# of samples) of bag -- overide in [BAGSIZE]
#name of the bag set if potentially combinding numerous sets
BAGSETNAME=GhanaJAB
#name for set of bags -- may be useful if multiple scans taking place
BAGNUM=1
# is the starting bag number which increments as bags fill
#regular expression to match within the barcode in the samplesheet AND the scanned barcode
# it will extract the first grouping "()"
# for example (P\d+) this allows P_32342-1 to match P32342-4
BARCODEMATCH=(P\d+)
#regular expression applied to scanned barcode and the sample file barcodes
#allows common code to be matched
[BAGSIZE]
#nondefault bagsize for bins above as well as BADBIN and BADCODE
GHANA = 100
MALAWI = 100
BADCODE=3
[BAGNUM]
#nodefault bag# to start at from bins above as well as BADBIN and BADCODE
GHANA = 100