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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified November 4, 2015
Description: Calculates EST (expressed sequence tags) capture by an assembly from a sam file.
Designed to use BBMap output generated with these flags: k=13 maxindel=100000 customtag ordered
Usage: bbest.sh in=<sam file> out=<stats file>
Parameters:
in=<file> Specify a sam file (or stdin) containing mapped ests.
out=<file> Specify the output stats file (default is stdout).
ref=<file> Specify the reference file (optional).
est=<file> Specify the est fasta file (optional).
fraction=0.98 Min fraction of bases mapped to ref to be
considered 'all mapped'.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
z="-Xmx120m"
z2="-Xms120m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function bbest() {
local CMD="java $EA $EOOM $z -cp $CP jgi.SamToEst $@"
# echo $CMD >&2
eval $CMD
}
bbest "$@"
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