[script-tokenizer]

#############################################################################
# 
# Hotspot/PTIH parameters file
#
# Note that variable substitution is allowed, using the %(_VARNAME_)s idiom.
# 
#############################################################################


#######################################
# Run-specific tokens
#######################################

# Location of tags bed file.  Must be at least 3-column (chrom, start,
# stop), although only the first two columns will be used.  May be
# compressed or uncompressed.  See  _UNCOMPR_ parameter below.
_TAGS_ = /home/rthurman/proj/hotspot-ptih/data/DNaseI.DS10081.5m.hg18.bed.gz

# Program to uncompress tags file, writing to stdout.  If tags file is
# already uncompressed, use "cat."
_UNCOMPR_ = zcat

# Hotspot creates and uses a simplified tags file, written to the
# following location.
_LIBD_ = /home/rthurman/proj/hotspot-ptih/pipeline-scripts/test

_GENOME_ = hg18

# k-mer size for input tags
_K_ = 27


# Include duplicate tags?  (T for DNaseI, F for ChIP)
_DUPOK_ = T

# Location of hotspot binary
_HOTSPOT_ = /home/rthurman/proj/hotspot-ptih/hotspot-deploy/bin/hotspot5

# Mappability files.  Hotspot uses information about what bases of the
# genome tags can be mapped to.  The files provided in the
# distribution are set up to assume that only uniquely-mappable bases
# are mapped to.
_MAPPABLE_FILE_ = /home/rthurman/proj/hotspot-ptih/data/%(_GENOME_)s.K%(_K_)s.mappable_only.bed
_MAPPABLE_10KB_FILE_ = /home/rthurman/proj/hotspot-ptih/data/k%(_K_)s.counts.10kb.total.summed

# Chromosome start/stop coordinates
_CHROM_FILE_ = /home/rthurman/proj/hotspot-ptih/data/chromInfo.%(_GENOME_)s.bed

# If _CHECK_ is T, hotspot will check output at various stages to see
# if results are computed for a particular chromosome (_CHKCHR_).
# This just provides an additional layer of checking.
_CHECK_ = T
_CHKCHR_ = X


##################################################################
# Standard algorithm parameters you probably will never mess with.
##################################################################

# Z-score threshold for hotspot detection
_THRESH_ = 2

# Hotspots within this distance will be merged
_MAX_WIN_ = 150

# Minimum hotspot width (bp)
_MINSIZE_ = 10

