#
# Notes
# -----
# All lines beginning with "#" are comments and ignored by the program.
# Removing or placing a "#" at the start will activate resp. silence that line.
#
# All strings (text in quotation marks) can be adapted but make sure to:
#     1. keep the quotation marks so that text stays of type string.
#     2. distinguish separate_WordsBy-otherMEANS than space, * | /\ $ : ; %
#     etc. (for file-handling).
# All numbers or True/False values can be changed (no surrounding quotes; these
#     are not strings).
#
# Save this file (EXPTXT) as unformatted text with "EXP" replaced by its value
# (ExpSessionName) set below, resulting in CONFNAM. This is done interactively
# when using the `coalispr init` command, including placing the file CONFNAM in
# the SAVEIN work folder.


# Name session/experiment "ExpSessionName"
# ----------------------------------------
# After editing is complete save this file as 3_ExpSessionName.txt in the same
# folder as the original. Replace "ExpSessionName" by one short word, no spaces
# or special characters (it is part of a file name), keep surrounding quotes.
# For "EXP" to be meaningful, strain names come to mind; e.g. JEC21, H99.
#EXP         = "ExpSessionName"
# Exp can be set by "coalispr init" with "yeast" as the given name.
EXP         = "yeast"
CONFNAM     = "3_yeast.txt"
# Display name for experiment is set to species name (not directly used),
EXPNAM      = "Saccharomyces cerevisiae"
# Display experiment name in figure titles
# ----------------------------------------
EXPDISP     = r'$\mathit{'+EXPNAM+'}$'
#
# Parameter settings
# ------------------
# The kind of aligned reads, either collapsed or uncollapsed, in the dataset.
# Values are TAGCOLL (collapsed) or TAGUNCOLL (uncollapsed) set in 2_shared.txt.
# Choose which segments of reads are counted; as based on kind of aligned reads.
TAGSEG      = TAGUNCOLL
# Choose which kind of bam files with aligned reads are counted.
# Counting collapsed reads is very fast, no information will be lost.
TAGBAM      = TAGCOLL
#
# To facilitate bedgraph comparison the genome needs to be split into fragments;
# BINSTEP is the size of these fragments;
# Note that this approach reduces nucleotide resolution to a scale 1:BINSTEP
# Reducing BINSTEP, to say 20, increases resolution but slows down proceedings.
BINSTEP     = 20
#
# UNSPECLOG10 is the log10 fold difference between specific peaks and unspecific
# background noise. For example with UNSPECLOG10 set to 1.3 = 10**1.3 = 19.95, a
# ~20-fold difference is used. This means that, in order to be specified as
# "specific", 20-fold more signal needs to be present in a bin for reads of a
# specific/mutant sample than in that bin for reads from a negative sample. If
# less signal-difference is found, these reads are specified as "unspecific" and
# ignored. When no reads are specified (no bedgraphs are drawn) reduce this
# number; it indicates that the experiment has a lower signal-to-noise ratio.
# For example with UNSPECLOG10 = 0.61, the required difference is ~4-fold.
UNSPECLOG10 = 0.905
# Series of possibilities for UNSPECLOG10
# values corresponding to ~4, ~6, ~8, 10, ~20 #, ~50, 100 fold difference
UNSPECTST   = 0.61, 0.78, 0.905, 1.0, 1.3 #, 1.7, 2.0
#
# 2**LOG2B (2^LOG2B) is background threshold above which reads in a bin are used.
LOG2BG      = 5           # 2**5 = 32
# Series of possibilities for LOG2BG
LOG2BGTST   = 4,5,6,7,8,9,10
#
# USEGAPS indicates the size of gaps tolerated between sections of a specified
# region/segment; 1*BINSTEP is the minimal gap that can be set. 
# For miRNAs BINSTEP seems a good choice; for large transcript regions targetted 
# by siRNAs a larger value is more fitting to reduce number of single hits.
USEGAPS     = BINSTEP #150         # 3*BINSTEP
# Keep unspecific signals as tight as possible, don"t fuse these.
UNSPCGAPS   = BINSTEP
# Series of possibilities for USEGAPS
UGAPSTST    = 50, 100, 150, 200, 300


# Bam-counting
# ------------
# For miRNAs single peaks can be expected. To score these for counting, expand
# hit coordinates by given, small fraction of BINSTEP (<1). 
MIRNAPKBUF  = 1/4  # 1/5 with BINSTEP 50; 1/4 for miRNA with BINSTEP 20.
# For siRNA analysis this buffer is less needed: siRNA peaks congregate and form 
# lengthy segments overlapping a target. Set to 0 to skip single peaks.
# The offsets define minimal length of region (2*BINSTEP*MIRNAPKBUF) to be 
# counted. BINSTEP is used when MIRNAPKBUF is set to 0.
#
# Alignment check
# +++++++++++++++
# Minimum length mapped read from (STAR) alignment or (Flexbar) trim parameters.
#XLIM0       = 12  # set in 'Settings for Figures'
#
# Setting to define sequencing type, single end (SE) vs paired-end  (PE)
#CNTTYP      = SE # if FLAG in [0,16], else
#CNTTYP      = PE
#
# Setting for expected alignment, that can be checked via the cigar string: 
# 'fully matched' (CIGFM) or 'with point deletions (CIGPD)' # see 2_shared.txt
# Cigar items as marked in 'cigartuples;cigarstring'
#   0;M, 1;I, 2;D, 3;N, 4;S, 5;H, 6;P, 7;=, 8;X, or 9;B
#   cigartuples = (operation, length)
#   # for short SE sequences only accept matches (0;M) and gaps (3;N)
#   # for UV-irradiated sequences with point deletions accept (0,2,3)
# For point-mutations (substitutions) (in UV-irradiated sequences) check, 
# separately, SAM-tag nM/NM via settings NM (in 2_shared.txt) and NRMISM.
#
# Set function to check cigar string with; for short RNAs:
CIGARCHK    = CIGFM # [0,3]
# Number of tolerated substitutions (mismatches) defined for NM:
NRMISM      = 0
# for UV-irradiated samples allow point-deletions (CRAC) or substitutions (CLIP)
# CIGARCHK    = CIGPD # [0,2,3] or [2,>1]
# NRMISM      = 1
#
# Minimum size for gap in alignment to count as "intron"
# During counting of bamfiles, gap sizes are read from the cigar string.
MININTRON   = 20
#
# BamCounters
# +++++++++++
# List of lists with counters for read numbers; (defined in "2_shared.txt")
CNTRS          = [CNTREAD, CNTCDNA, CNTGAP, CNTSKIP]
# List of length-counters' lists; (subsets defined in "2_shared.txt")
LENCNTRS       = [LENREAD, LENCDNA, LENGAP]
# For counting  multimap occurrences (defined in "2_shared.txt")
MMAPCNTRS      = [ [LIBR, INTR] ]
# Omit counting introns/gaps: 
#CNTRS          = [CNTREAD, CNTCDNA, CNTSKIP]
#LENCNTRS       = [LENREAD, LENCDNA]
#MMAPCNTRS      = [ [LIBR] ]
#
# Segments
# ++++++++
# BINS is the number of bins (1 or over) to split a specified segment into for
# which reads are counted. This might help to map possible coverage differences
# dependent on conditions, say the effect of isolating RNA via RIP1 vs. RIP2).
# When the length of a counted segment is shorter than BINSTEP*BINS, no division
# into BINS occurs; this to prevent creating smaller segments than the BINSTEP  
# used for collecting data.
BINS        = 1
#
# Reads in UNSPECIFIC segments that comply with SPECIFIC small RNA
# characteristics can be retrieved and copied to new bam files for further
# analysis/mapping. These reads are called "unselected" reads.
# Define here the length range and start nucleotide for such reads. The range
# is a tuple, that is: Shortest length (BAMLOW), Longest length (BAMHIGH).
BAMLOW      = 19
BAMHIGH     = 25
BAMPEAK     = BAMLOW, BAMHIGH
# List of start nucleotides; 5" end of siRNAs in fungi are U (T in the reads).
BAMSTART    = "T"
# Name of bash script to make bedgraphs from above new bam files using STAR.
BAM2BGNAM   = "bm2bg.sh"
# Path to script
BAM2BG = p / "share" / "bash_scripts" / BAM2BGNAM


# Settings for Figures
# --------------------
# Correct chromosome name when displaying bedgraph traces with `showgraphs` by
# adjusting x-axis label
CHROMLBL    = "Chromosome"
#CHROMLBL    = ""
#
# Length boundaries of introns (gaps in alignment) to be displayed in figures.
MINGAP      = 30 #MININTRON
MAXGAP      = 150 
# Interval for tick-labels on x-axis for intron-length distributions.
INTSTEP     = 10
# Set interval of lengths without data to skip
SKIPINT      = "" 
#SKIPINT    = 190, 350
# Length boundaries of reads to be displayed in count figures
XLIM0       = 12 # minimum mapping length
XLIM1       = 40
XLIM00      = 16
XLIM11      = 26
XLIMMIN     = 12 # minimal length of a mapped read
XLIMMAX     = 75 # maximum length of a read
# Allow separate constants for region length-distributions.
XLIMR0      = XLIM00
XLIMR1      = XLIM11
# Factor defining relative height of sample-panes in bardiagrams
# for many samples a low CPPHFAC keeps the figure managable
# Library counts (CountPanelPlotter)
CPPHFAC     = 1/8 #0.125
# Length distributions of reads or introns/gaps ((Broken)LengthPanelPlotter)
LPPHFAC     = 1/5 #0.2    #1/4 #0.25   #3/8  #0.375
# When assembling stacked panels for all samples, the total height of the 
# longest column defines the figure; with too many samples the figure runs off 
# the page. Setting MAXROW determines how many samples are tolerated before
# this column is split in two (non-equal) stacks. 
MAXROW      = 30


# Datafile folders and names
# --------------------------
# Default directory structure:
# full path to bedgraph and bam files:
# BASEDIR / SRCFLDR+tag / FILEKEY* / FILEKEY*BEDGRAPH
# BASEDIR / SRCFLDR+tag / FILEKEY* / BAM
# SRCDIR = BASEDIR / SRCFLDR+tag
# BASEDIR = Path(SETBASE)
#
# SETBASE is the string giving the absolute or full path to the base directory
# with input sequencing data. This directory contains SRCFLDR+tag
# folders for either collapsed- or uncollapsed-read alignments, which -in turn-
# contain (links to) FILEKEY folders with bedgraph and bam files.
SETBASE     = "/home/working/DATA_ANALYSIS_2/Kre33Puf6/"
# SETBASE    = ""
#
# SRCFLDR is name of the folder containing folders with bedgraphs, which are
# based on alignments to a particular reference genome, which depends on EXP.
# When replacing the name, keep underscore at end (the "collapsed" or
# "uncollapsed" tag will get attached here)
# The string "0" reflects that zero mismatches were tolerated during mapping of
# the reads after adapter removal.
MUTNO       = "1"
SRCFLDR     = "STAR-analysis" + MUTNO + "-" + EXP + "_"
#
# Folder with downloaded reference RNA-seq bedgraph-files (separate from data)
# If in a sub-directory of the source folder: ( SRCFLDR / REFS )
# If in a top-level directory (BASEDIR / REFS ; or REFS )
#REFS        = "REFS"
#REFS        = ""
# Self-processed reference RNA-seq bedgraph-files in folder alongside data.
# Rename Sra RUNs after downloading data to enable specific alignment parameters
# (settings for mapping reference mRNA will differ from those for small RNA).
REFNAM      = "refSRR4024831_"
REFS        = REFNAM + tag + "_" + MUTNO + "mismatch-" + EXP

#
# File extension used for bedgraph files; note the connecting dot
BEDGRAPH    = ".bedgraph"
#BEDGRAPH    = ".bg"
#
# Label in bedgraph filename to indicate data for uniq reads only
# (An aligner as STAR can create such files). These files will be ignored
# unless they are the only ones available.
#UNIQ        # also used for count-file name; set in "2_shared.txt"
#
# Marker for upper, top, left-hand, 1, Watson, reference, (+) strand
# Cartwright and Graur 2011, http://www.biology-direct.com/content/6/1/7
# Used for file naming when writing/saving.
PLUS        = "plus"
# Marker for lower, bottom, right-hand, 2, Crick, (-) strand
MINUS       = "minus"
#
# Markers for PLUS, MINUS as available in names of input bedgraph files.
PLUSIN      = PLUS
MINUSIN     = MINUS
#
# Abbreviated strand-naming during storage via prefixes;
# for PLUS
PL          = "p"
# for MINUS
MI          = "m"
#
# Common/shared name for alignment files with .bam extension as generated by
# `samtools sort` and needed for indexing. Thus the same bam-file name covers
# the alignments for different experiments; therefore the name of the folder
# containing the generated bam-file (FILEKEY*) is used as the distinguishing
# factor.
BAM         = "samtoolsAligned.sortedByCoord.out.bam"
#
# Filename of unmapped reads, filtered out of the sequencing data by alignment;
# an aligner as STAR saves this as a separate file, which can be compresssed.
UNMAPPEDFIL = "Unmapped.out.mate1.gz"
#
# Countable filetypes of unmapped output.
# After mapping by STAR, files with unmapped data (UNMAPPEDFIL) are saved in
# either the format of fastq (with uncollapsed data) or of fasta (with collapsed
# output from pyFastqDuplicateRemover.py from pyCRAC). Therefore:
# for uncollapsed reads unmapped output is of type:
UNMAPTYPE   = "fastq"
# for collapsed reads unmapped output is of type:
UNMAPCOLLTP = "fasta"
# With another aligner that would count unmapped reads, these might be
# retrievable from the SAM.header if these are saved therein. Otherwise
# unmapped read numbers have to be retrieved by other means if unmapped reads
# are not output in fastq or fasta format.


# Experiment file
# ---------------
# EXPFILNAM gives the path to the "experiment file" describing sequencing data.
#EXPFILNAM   = ""
EXPFILNAM   = "Kre33Puf6_Exp.tsv"

# Column headers
# ++++++++++++++
# Headers of expected columns in an experiment file.
#
# FILEKEY is a column of identifiers that link to folders with BEDGRAPH and
# BAM files. When downloading data from GEO with the sra-toolkit, a "Run" 
# column with SRA accession numbers is present in the 'SraRunTable.txt'.
# The expected folder hierarchy is then formed automatically, so that 
# the SRR names of folders can be directly used as links to the data.
FILEKEY     = "Run"
#
# SHORT is a column of memorable abbreviations as names for samples used in the
# display and for comparing bedgraphs.
SHORT       = "Short"
#
# CATEGORY divides samples according to their roles (see below)
CATEGORY    = "Category"
#
# EXPERIMENT gives a longer description than the SHORT name and possibly more
# informative than the FILEKEY. Basically for understanding the table in the
# file; not used in the program.
EXPERIMENT  = "Description"
#
# Use GROUP for keeping comparable mutations together. The various GROUPS (see
# below) can be redefined for displaying a longer name than the short version.
GROUP       = "Group"
#
# CONDITION defines environmental or genetic changes (see below)
# CONDITION is defined in "2_shared.txt" as plot label
#
# READDENS values are integers indicating relative density of Reference reads;
# these numbers are used to transform (or level up) overall peakheight of traces
# for reference RNA-seq libraries to allow for an easier visual comparison.
READDENS    = "Read-density"
#
# METHOD describes RNA preparation method (see below)
# METHOD    is defined in "2_shared.txt" as plot label
#
# FRACTION 
# FRACTION    is defined in "2_shared.txt" as plot label

# Column Values
# +++++++++++++
# The labels put in various columns to describe the sample
#
# FILEKEY column
# **************
# These values are as the beginning of bedgraph file-names and of the name of
# the sub-folder where the bedgraphs and alignment file are stored.
#
# SHORT column
# ************
# These values are the shortest possible abbreviation for a sample. Replicates
# of the same experiment should be divided from the short name by means of an
# underscore (_). This enables to display the technical (character) or
# biological (number) replicates of the same experiment as one group. Thus
# three wild-type replicates with SHORT names "wt_1a", "wt_2", "wt_1c" can be
# marked as "wt" in the GROUP column and then displayed as one group named "wt".
#
# CATEGORY column
# ***************
# These values specify the samples and direct how they get sorted/used.
# For Reference
CAT_R       = "R"
# For Unspecific i.e. negative control
# use lowercase for negative controls not used for defining 'UNSPECIFIC' reads
CAT_U       = "U"
# For Specific i.e. positive control
# use lowercase for positive controls not used for defining 'SPECIFIC' reads
CAT_S       = "S"
# For Mutant
# use lowercase for redundant samples not considered for bedgraph display
CAT_M       = "M"
# For Discard
CAT_D       = "D"
#
# METHOD column
# *************
# These values indicate the kind of experiment used for preparing the RNA
# input sample that has been sequenced. RIP, RNA extracted from
# immunoprecipitated proteins (IPs), give less/different background than
# sequences from total RNA preps, for which only a size-enrichment step can be
# applied.
# For reads from a total sRNA seq prep
TOTAL       = "rip3" ## for nab3-crac instead of "total"
# For reads from a RNA IP sample
RIP1        = "rip33" ## kre33-crac
RIP2        = "rip6"  ## puf6-crac
# For reads from a RNA IP beads/untagged control (found to be unusable as CAT_U;
# mostly CAT_D)
NOTAGIP     = "rip0"
#
# GROUP column
# ************
# These values will normally be the first part of the associated and
# comparable short names of a mutant, say a2 for a2_2, a2_1, a2_3ms0 samples.
# Other labels for a group of mutants could reflect a shared role.
# In this example for reads in mutants linked to DNA or histone methylation.
OTHR        = "meth"
#
# CONDITION column
# ****************
# Entries are optional; values will be extracted from the EXPFILE when needed.
#
# Values reflect different grow or genetic conditions that could affect
# phenotype, i.e. the kind of RNA produced that would be sequenced.
# For example a genetic modification with huge impact:
# Mutant made in RNAi-null parental strain. (REPAIR is not used in source code.)
REPAIR      = "rep"
# An example of an environmental change that can be expected to have an impact:
# Samples from Murashige and Skoog starvation medium (MS0) kept in the dark,
# described as stimulating mating, and spore formation, under which RNAi-
# proteins become more abundant in Cryptococcus (doi:10.1101/gad.1970910).
# (STARV as constant, is not used in source code.)
STARV       = "ms0"
# Samples that have been grown to a very high density possible leading to
# quorum or nutritional stress. (DENSE as constant, is not used in source code.)
DENSE       = "highOD"
# Samples not annotated are considered to represent the same standard condition
# and are referred to with constant REST (which is used in source code).
REST        = "standard"
#
# FRACTION column
# ***************
# These values reflect which fractions of a biological sample have been used for
# preparing the RNA
#Whole cell extract
WCE         = "WCE"
#Nucleolus
NUCLEO      = "Nucleo"
NUCL        = "Nuc"
# Cytosol, cytoplasmic
CYTO        = "Cyt"
MITOCH      = "Mit"
MEMBR       = "Mem"
VACUOL      = "Vac"
GRANUL      = "P-body"
#Endoplasmic reticulum
ENDRET      = "ER"
#Extracellular
EXCELL     = "Medium"

# Groups definitions
# ------------------
# A dictionary, key (= "SHORT label in EXPFILE") : value ("displayed");
#
# For a functional presentation order (not alphabetical) and to provide extra 
# description for short names (**SHORT**) when displaying values of a GROUP  
# column alongside bedgraph traces; these will form side-panel titles.
#
# Only replace key/value labels, keep { }, quotes " ", colon : and commas 
# between key:value entries.
# '\u0394' is unicode for the delta symbol; '\u03B2' for beta; '\u2192', arrow.
MUTGROUPS   = ""
#MUTGROUPS   = {  
#               "K33" : "Kre33",  
#               "P6" : "Puf6",  
#               "N3" : "Nab3",
#              }


# Other possible groups for the side panel legend, defines labels and order of
# presentation/appearance.
# Use (remove # sign) "" lines if only one condition or method has been tested
# and remove (comment out) lines with different conditions or different methods.

CONDITIONS  =  ""
#METHODS     =  ""
#FRACTIONS   =  ""

#CONDITIONS  = {
#               REPAIR:"repaired", STARV:"starved", DENSE:"high OD"
#              }
METHODS     = {
                TOTAL:"Nab3 crac", RIP1:"Kre33 crac", RIP2:"Puf6 crac",
              }
FRACTIONS   = {
                WCE:"Cell extract",
              }

# define (display order of) mutant-groups for CAT_M and CAT_U
UNSPECIFICS = [
               "N3",
              ]
MUTANTS     =  ""
#MUTANTS     = [
#               "K33", "P6", "N3", 
#              ]


# Genome info
# -----------
# genome info; all files should be placed in the "config/source" folder;
# use "" if not applicable (remove # at beginning); remove or comment out
# example line (place # at beginning)
LENGTHSNAM = "Saccharomyces_cerevisiae.R64-1-1.75_chromosome_lengths.txt"
# when features omitted from the reference genome are described 
# in additional fasta and gtf files; these sequences are counted as genomic
# Name for "chromosome" with additional genomic DNA sequences;
ADD_GDNA  = "" #"MitochCneoD"
# Name for file with DNA sequence additional genomic DNA
GDNA_FILNAM = "" #"MitochCneoD.fa"
# Length of additional genomic DNA sequence
LEN_GDNA  = ""
# Name of file with length of additional genomic DNA sequence
LEN_GDNAFILNAM = ""
# When extrageneous DNA, like mutational sequences, are described in different 
# fasta and gtf files; counts for these sequences are treated separately:
# Name for extra "chromosome" with additional or mutational DNA sequences;
DNAXTRNAM  = "" #MitochCneoDTagsRecombinationalDNAs.fa"
LENXTRFILNAM = "" #MitochCneoDTagsRecombinationalDNAs-lengths.txt"
#LENGTHSFILE = ""
LENXTRA     = "" # 43824   # same value as in LENXTRAFILE;
# Name for extra "chromosome" with additional or mutational DNA sequences;
CHRXTRA     = ""
#CHRXTRA     = XTRA # "extra", set in "2_shared.txt";
# Annotation files to be used for gtf-tracks in bedgraph display
# use "" if not applicable
GTFSPECNAM  = "" #Saccharomyces_cerevisiae.R64-1-1.75_1.2.gtf"
GTFUNSPNAM  = "" #Cryptococcus_neoformans.ASM9104v1.ncrna__db.gtf"
GTFREFNAM   = "Saccharomyces_cerevisiae.R64-1-1.75_1.2.gtf"
# GTF files that annotates additional "chromosomes", ADD_GDNA or CHRXTRA;
# For extension of reference GTF
GTFGDNANAM  = "" #"MitochCneoD.gtf"
GTFXTRANAM  = "" #"TagsRecombinationalDNAs-genes_exons_cds.gtf"
# For extension of GTFUNSPNAM GTF with common non-coding RNAs
GTFUNGDNANAM = "" #
GTFUNXTNAM  = ""
#

# In case other keywords are used to describe most relevant feature in GTF
GTFEXON     = "exon"        # kind of annotated feature to display
GTFFEAT     = "sirnasegment" # feature of choice to display


# Work-folder for storing configuration, logs, figures and data
# -------------------------------------------------------------
# Generated from above settings:
BASEDIR     = Path(SETBASE)
# Where to store outputs from ("data") and configuration files for the program
# (the EXPFILE, "2_shared.txt" and "3_EXP_.txt" files)
# Generated after init:
# User home directory, similar to choice "home folder" during "coalispr init".
#SAVEIN      = Path.home() / PRGNAM
# Near sequencing files, as choice "current directory" during "coalispr init".
#SAVEIN      = BASEDIR / PRGNAM
# Next to program folder, like "source folder" choice during "coalispr init".
#SAVEIN      = p.parent.parent
# Set by "coalispr init" to /home/working/DATA_ANALYSIS_2/Kre33Puf6/Coalispr
SAVEIN      = Path("/home/working/DATA_ANALYSIS_2/Kre33Puf6/Coalispr")

# Within program source folder "resources/" (remnant from development)
#CONFIG      = p
# In config subfolder (default)
CONFIG      = SAVEIN / CONFBASE

LENGTHSFILE = BASEDIR / LENGTHSNAM
#LENGTHSFILE = BASEDIR / SOURCE / LENGTHSNAM
#LENGTHSFILE = ""
#
GDNA_FILE = ""
#GDNA_FILE = "BASEDIR / GDNA_FILNAM"
#GDNA_FILE = "BASEDIR / SOURCE / GDNA_FILNAM"
LEN_GDNAFILE = ""
#LEN_GDNAFILE = "BASEDIR / LEN_GDNA_FILNAM"
#LEN_GDNAFILE = "BASEDIR / SOURCE / LEN_GDNA_FILNAM"
#
DNAXTRA     = ""
#DNAXTRA     = BASEDIR / DNAXTRNAM
#DNAXTRA     = BASEDIR / SOURCE / DNAXTRNAM
LENXTRAFILE = ""
#LENXTRAFILE = BASEDIR / LENXTRFILNAM
#LENXTRAFILE = BASEDIR / SOURCE / LENXTRFILNAM

# Next or near to sequencing data
EXPFILE     =  BASEDIR / EXPFILNAM
#EXPFILE     =  BASEDIR / SOURCE / EXPFILNAM
# In/next to configuration folder 
#EXPFILE     = CONFIG / EXPFILNAM
CONFPATH    = CONFIG / CONFFOLDER
CONFFILE    = CONFPATH / CONFNAM
OUTPATH     = SAVEIN / OUTPUTS / EXP
STOREPATH   = SAVEIN / DATA / EXP
# Parent-folder(BASEDIR)/tag folder/exp-folder/exp-bedgraph-files
# Data source directory is set by program to BASEDIR / (SRCFLDR + tag)
# Parent-folder(BASEDIR/REFS)/reference-folder/reference-bedgraph-files
#REFDIR      = BASEDIR / REFS
REFDIR      = SRCDIR / REFS   ## REFNDIRLEVEL= 0
# Number of folders between REFDIR and bedgraph files
REFNDIRLEVEL= 0

GTFSPEC     = ""
#GTFSPEC     = BASEDIR / SOURCE / GTFSPECNAM
GTFUNSP     = ""
#GTFUNSP     = BASEDIR / SOURCE / GTFUNSPNAM
#GTFREF      = ""
GTFREF      = BASEDIR / GTFREFNAM
#GTFREF      = BASEDIR / SOURCE / GTFREFNAM
# For extension of reference GTF
GTFGDNA     = ""
#GTFGDNA     = BASEDIR / GTFGDNANAM
#GTFGDNA     = BASEDIR / SOURCE / GTFGDNANAM
GTFXTRA     = ""
#GTFXTRA     = BASEDIR / GTFXTRANAM
#GTFXTRA     = BASEDIR / SOURCE / GTFXTRANAM
# For extension of GTFUNSPNAM GTF with common non-coding RNAs
GTFUNGDNA     = ""
#GTFUNGDNA     = BASEDIR / GTFUNGDNANAM
#GTFUNGDNA     = BASEDIR / SOURCE / GTFUNGDNANAM
GTFUNXTR    = ""
#GTFUNXTR    = BASEDIR / GTFUNXTNAM
#GTFUNXTR    = BASEDIR / SOURCE / GTFUNXTNAM

# Figure paths
FIGDIRSVG   = SAVEIN / FIGS / EXP / SAVESVG
FIGDIRPNG   = SAVEIN / FIGS / EXP / SAVEPNG
FIGDIRPDF   = SAVEIN / FIGS / EXP / SAVEPDF
FIGDIRJPG   = SAVEIN / FIGS / EXP / SAVEJPG
# Set here preferred default:
FIGDIR      = FIGDIRSVG

# Debug log
LOGFIL      = SAVEIN / LOGS / EXP / LOGFILNAM
