[script-tokenizer]

#######################################
## Notes:  If duplicate token definitions exist, the last definition in
##         the file will be used. Tokens can use .ini variables and declarations.
##         See http://docs.python.org/library/configparser.html
#######################################

#######################################
# Global tokens (used by most scripts)
#######################################

## Tags file in bam format (file extension .bam), or starched bed file
## (file extension .bed.starch).  If the tags file is in bed.starch
## format, and if it is in directory specified by _OUTDIR_, then it
## needs to be in the format
##
##     chr  5'start  5'start+1
##
## That is, the file should be three column bed (no ID field, etc.)
## containing the 1bp coordinates of the 5' ends of the tags. If
## _TAGS_ is a bam file, or a bed.starch file not in _OUTDIR_, then
## the bed.starch file in the above format will be generated (using
## the strand column if present), and put in _OUTDIR_.  NOTE: if you
## use run_badspot, then you must use bam files, or a bed.starch file
## not in _OUTDIR_.

_TAGS_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/data/NHDF_Ad.DNase_seq.hg19.bam

## For ChIP data with an Input bam file, set _USE_INPUT_ to T, and set
## _INPUT_TAGS_ to the name of that bam file.

_USE_INPUT_ = F 
_INPUT_TAGS_ = 

## Genome 
_GENOME_ = hg19
## Tag length
_K_ = 36
## Chromosome coordinates, bed format.
_CHROM_FILE_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/data/hg19.chromInfo.bed
## Location of uniquely mappable positions in the genome for this tag length.
_MAPPABLE_FILE_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/data/hg19.K36.mappable_only.bed.starch

## Set DUPOK to T for DNaseI data, F for ChIP-seq data (DUPOK = T means allow duplicate reads)
_DUPOK_ = T

## FDR levels, separated by spaces if more than one. Set to N if you
## do not want FDR thresholding (for example, if you just want SPOT
## score computed.)  
## _FDRS_ = "N"
_FDRS_ = "0.01"

## Tag density, 150bp window, sliding every 20bp, used for
## peak-finding.  Will be generated, based on the _TAGS_ file, if it
## does not exist. Assumed to be starched bed file, extension
## bed.starch.  Can be blank, in which case the density file will be
## generated in _OUTDIR_, and the the name will be the name of the
## tags file, minus the bam or bed.starch extension, with the added
## extension tagdensity.bed.starch.  
_DENS_:

## Output directories (can all be the same location).  Use full path names.
## _OUTDIR_ contains tags files in converted bed.starch and lib.txt formats (for hotspot
## program), and hotspot and peak results.
## _RANDIR_ contains generated random tags (for FDR thresholding) and hotspots called on random tags.
_OUTDIR_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/pipeline-scripts/test
_RANDIR_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/pipeline-scripts/test

## If there are any regions from which tags should be automatically
## omitted, include those here (only if you use run_badspot). May be
## left blank.
_OMIT_REGIONS_: /woldlab/castor/home/georgi/programs/hotspot-distr-v4/data/Satellite.hg19.bed

## Set to T if you want scripts to skip steps that have already been done.
_CHECK_ = T

## If _CHECK_ = T, outputs are checked for completeness by searching
## for results for the following chromsome.
_CHKCHR_ = chrX

## Hotspot program binary
_HOTSPOT_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/hotspot-deploy/bin/hotspot

## Clean up. Remove all intermediate files and directories if set to T.  See
## pipeline script run_final.
_CLEAN_ = T

## Peak-finding program.
_PKFIND_BIN_ = /woldlab/castor/home/georgi/programs/hotspot-distr-v4/hotspot-deploy/bin/wavePeaks
## Peak-finding smoothing level. If the resolution of the input file
## is x, then the results are smoothed out to a scale of (2^level)*x.
_PKFIND_SMTH_LVL_ = 3

## Random number seed, used for generating random tags for FDR thresholding.
_SEED_=101

## Hotspot program parameters
_THRESH_ = 2
_WIN_MIN_ = 200
_WIN_MAX_ = 300
_WIN_INCR_ = 50
_BACKGRD_WIN_ = 50000
_MERGE_DIST_ = 150
_MINSIZE_ = 10