jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified May 23, 2014
jpayne@69: 
jpayne@69: Description:  Grades mapping correctness of a sam file of synthetic reads with headers generated by RandomReads3.java
jpayne@69: 
jpayne@69: Usage:   gradesam.sh in=<sam file> reads=<number of reads>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       Specify the input sam file, or stdin.
jpayne@69: reads=<int>     Number of reads in mapper's input (i.e., the fastq file).
jpayne@69: thresh=20       Max deviation from correct location to be considered 'loosely correct'.
jpayne@69: blasr=f         Set to 't' for BLASR output; fixes extra information added to read names.
jpayne@69: ssaha2=f        Set to 't' for SSAHA2 or SMALT output; fixes incorrect soft-clipped read locations.
jpayne@69: quality=3       Reads with a mapping quality of this or below will be considered ambiguously mapped.
jpayne@69: bitset=t        Track read ID's to detect secondary alignments.
jpayne@69:                 Necessary for mappers that incorrectly output multiple primary alignments per read.
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: 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: function gradesam() {
jpayne@69: 	local CMD="java $EA $EOOM -Xmx200m -cp $CP align2.GradeSamFile $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: gradesam "$@"