<commit_before>#!/bin/bash

version="1.0.0"



EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
platform='mac'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
   platform='linux'
fi

dsk_bin=$EDIR/thirdparty/dsk/bin/macosx/dsk
if [[ $platform == 'linux' ]]; then
       dsk_bin=$EDIR/thirdparty/dsk/bin/linux/dsk
fi
chmod a+x ${dsk_bin}


#BIN DIR:
if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
       BIN_DIR=$EDIR/build/bin
else # VERSION BINARY
       BIN_DIR=$EDIR/bin
fi


function help {
echo "long_read_connector.sh - Groups reads within a RNA read set."
echo "Version "$version
echo "Usage: sh short_read_connector.sh -b read_file_of_files [OPTIONS]"
echo  "MANDATORY:"
echo  "	-f read_file_of_files for bank"
echo  "	  Example: -b data/c1.fasta.gz"

echo  "OPTIONS:"
echo  "	-p prefix. All out files will start with this prefix. Default=\"short_read_connector_res\""
echo  "	-g: with this option, if a file of solid kmer exists with same prefix name and same k value, then it is re-used and not re-computed."
echo  "	-k value. Set the length of used kmers. Must fit the compiled value. Default=21"
echo  "	-F value. Fingerprint size. Size of the key associated to each indexed value, limiting false positives. Default=12"
echo  "	-G value. gamma value. MPHF expert users parameter - Default=2"
echo  "	-a: kmer abundance min (kmer from bank seen less than this value are not indexed). Default=2"
echo  "	-s: Minimal percentage of shared kmer in a region for considering 2 reads in a same group. Default=75"
#~ echo  " -w: Region (putative exon) size. Default=80"
echo  "	-t: number of thread used. Default=0"
}



bank_set=""
query_set=""
kmer_size=21
abundance_min=2
gamma=10
fingerprint_size=32
kmer_threshold=75
core_used=4
prefix="long_read_connector_res"
remove=1
diskMode=0
countMode=0

small_k=9
nb_small_k=30
size_windows=80

#######################################################################
#################### GET OPTIONS                #######################
#######################################################################
while getopts "hgf:q:p:k:a:s:w:t:F:G:K:N:W:" opt; do
case $opt in

h)
help
exit
;;<commit_msg> re set defaut param for core used<commit_after>#!/bin/bash

version="1.0.0"



EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
platform='mac'
unamestr=`uname`
if [[ "$unamestr" == 'Linux' ]]; then
   platform='linux'
fi

dsk_bin=$EDIR/thirdparty/dsk/bin/macosx/dsk
if [[ $platform == 'linux' ]]; then
       dsk_bin=$EDIR/thirdparty/dsk/bin/linux/dsk
fi
chmod a+x ${dsk_bin}


#BIN DIR:
if [ -d "$EDIR/build/" ] ; then # VERSION SOURCE COMPILED
       BIN_DIR=$EDIR/build/bin
else # VERSION BINARY
       BIN_DIR=$EDIR/bin
fi


function help {
echo "long_read_connector.sh - Groups reads within a RNA read set."
echo "Version "$version
echo "Usage: sh short_read_connector.sh -b read_file_of_files [OPTIONS]"
echo  "MANDATORY:"
echo  "	-f read_file_of_files for bank"
echo  "	  Example: -b data/c1.fasta.gz"

echo  "OPTIONS:"
echo  "	-p prefix. All out files will start with this prefix. Default=\"short_read_connector_res\""
echo  "	-g: with this option, if a file of solid kmer exists with same prefix name and same k value, then it is re-used and not re-computed."
echo  "	-k value. Set the length of used kmers. Must fit the compiled value. Default=21"
echo  "	-F value. Fingerprint size. Size of the key associated to each indexed value, limiting false positives. Default=12"
echo  "	-G value. gamma value. MPHF expert users parameter - Default=2"
echo  "	-a: kmer abundance min (kmer from bank seen less than this value are not indexed). Default=2"
echo  "	-s: Minimal percentage of shared kmer in a region for considering 2 reads in a same group. Default=75"
#~ echo  " -w: Region (putative exon) size. Default=80"
echo  "	-t: number of thread used. Default=0"
}



bank_set=""
query_set=""
kmer_size=21
abundance_min=2
gamma=10
fingerprint_size=32
kmer_threshold=75
core_used=0
prefix="long_read_connector_res"
remove=1
diskMode=0
countMode=0

small_k=9
nb_small_k=30
size_windows=80

#######################################################################
#################### GET OPTIONS                #######################
#######################################################################
while getopts "hgf:q:p:k:a:s:w:t:F:G:K:N:W:" opt; do
case $opt in

h)
help
exit
;;
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