<commit_before># author: <NAME>
# date: June 2014

#####################################
# Resources
#####################################

#********************
# Tasks 
#********************

# list of task to put into report
RUNHOTSPOT="1"   

#********************
# Paths
#********************

SOURCE=$(pwd)

# which folder to run on (i.e. folders within fastq directory)
declare -a DIR; DIR=( sample1 sample2 )

# folder/task containing the data this task operates on
INPUT_HOTSPOT=$TASK_BOWTIE

# reference genome, 
# e.g. /share/ClusterShare/biodata/contrib/genomeIndices_garvan/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.fa
# or   ${NGSANE_REFERENCE}/b37/human_g1k_v37.fasta
FASTA=

# where to write the output
OUT=$SOURCE

# where to write the log files
QOUT=$OUT/qout

#********************
# PARAMETER (mandatory)
#********************

# UCSC genome assembly 
# e.g. UCSC_GENOMEASSEMBLY="hg19"
UCSC_GENOMEASSEMBLY=

# Tokenizer config file
read -d '' HOTSPOTCONFIG <<HOTSPOT_CONFIG_END
_USE_INPUT_ = F
## Genome assembly
_GENOME_ = $UCSC_GENOMEASSEMBLY
## Tag length
_K_ = 36
## Chromosome coordinates, bed format.
_CHROM_FILE_ = $HOTSPOT_HOME/data/$UCSC_GENOMEASSEMBLY.chromInfo.bed
## Location of uniquely mappable positions in the genome for this tag length.
_MAPPABLE_FILE_ = $HOTSPOT_HOME/data/$UCSC_GENOMEASSEMBLY.K36.mappable_only.bed.starch
#Duplication
_DUPOK_ = T
_FDRS_ = "0.01"
_DENS_:
_OMIT_REGIONS_: $HOTSPOT_HOME/data/Satellite.$UCSC_GENOMEASSEMBLY.bed
_CHECK_ = T
_CHKCHR_ = chrX
_HOTSPOT_ = $HOTSPOT_HOME/bin/hotspot
_CLEAN_ = T
_PKFIND_BIN_ = $HOTSPOT_HOME/bin/wavePeaks
_PKFIND_SMTH_LVL_ = 3
_SEED_=101
## Hotspot program parameters
_THRESH_ = 2
_WIN_MIN_ = 200
_WIN_MAX_ = 300
_WIN_INCR_ = 50
_BACKGRD_WIN_ = 50000
_MERGE_DIST_ = 150
_MINSIZE_ = 10
HOTSPOT_CONFIG_END<commit_msg>Bugfix multi-line variable handling<commit_after># author: <NAME>
# date: June 2014

#####################################
# Resources
#####################################

#********************
# Tasks 
#********************

# list of task to put into report
RUNHOTSPOT="1"   

#********************
# Paths
#********************

SOURCE=$(pwd)

# which folder to run on (i.e. folders within fastq directory)
declare -a DIR; DIR=( sample1 sample2 )

# folder/task containing the data this task operates on
INPUT_HOTSPOT=$TASK_BOWTIE

# reference genome, 
# e.g. /share/ClusterShare/biodata/contrib/genomeIndices_garvan/iGenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.fa
# or   ${NGSANE_REFERENCE}/b37/human_g1k_v37.fasta
FASTA=

# where to write the output
OUT=$SOURCE

# where to write the log files
QOUT=$OUT/qout

#********************
# PARAMETER (mandatory)
#********************

# UCSC genome assembly 
# e.g. UCSC_GENOMEASSEMBLY="hg19"
UCSC_GENOMEASSEMBLY=

# Tokenizer config file
HOTSPOTCONFIG=$(cat << HOTSPOT_CONFIG_END
_USE_INPUT_ = F
## Genome assembly
_GENOME_ = $UCSC_GENOMEASSEMBLY
## Tag length
_K_ = 36
## Chromosome coordinates, bed format.
_CHROM_FILE_ = $HOTSPOT_HOME/data/$UCSC_GENOMEASSEMBLY.chromInfo.bed
## Location of uniquely mappable positions in the genome for this tag length.
_MAPPABLE_FILE_ = $HOTSPOT_HOME/data/$UCSC_GENOMEASSEMBLY.K36.mappable_only.bed.starch
#Duplication
_DUPOK_ = T
_FDRS_ = "0.01"
_DENS_:
_OMIT_REGIONS_: $HOTSPOT_HOME/data/Satellite.$UCSC_GENOMEASSEMBLY.bed
_CHECK_ = T
_CHKCHR_ = chrX
_HOTSPOT_ = $HOTSPOT_HOME/bin/hotspot
_CLEAN_ = T
_PKFIND_BIN_ = $HOTSPOT_HOME/bin/wavePeaks
_PKFIND_SMTH_LVL_ = 3
_SEED_=101
## Hotspot program parameters
_THRESH_ = 2
_WIN_MIN_ = 200
_WIN_MAX_ = 300
_WIN_INCR_ = 50
_BACKGRD_WIN_ = 50000
_MERGE_DIST_ = 150
_MINSIZE_ = 10
HOTSPOT_CONFIG_END
)
{'fraction_non_alphanumeric': 0.19130434782608696, 'fraction_numerical': 0.025, 'mean_word_length': 5.906191369606003, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6580679', 'n_tokens_mistral': 1556, 'n_tokens_neox': 1420, 'n_words': 294}