jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified November 4, 2015
jpayne@69: 
jpayne@69: Description:  Calculates EST (expressed sequence tags) capture by an assembly from a sam file.
jpayne@69: Designed to use BBMap output generated with these flags: k=13 maxindel=100000 customtag ordered
jpayne@69: 
jpayne@69: Usage:        bbest.sh in=<sam file> out=<stats file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       Specify a sam file (or stdin) containing mapped ests.
jpayne@69: out=<file>      Specify the output stats file (default is stdout).
jpayne@69: ref=<file>      Specify the reference file (optional).
jpayne@69: est=<file>      Specify the est fasta file (optional).
jpayne@69: fraction=0.98   Min fraction of bases mapped to ref to be 
jpayne@69:                 considered 'all mapped'.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx120m"
jpayne@69: z2="-Xms120m"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: function bbest() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.SamToEst $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: bbest "$@"