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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified March 21, 2018
Description: Converts sam/bam to fastq rapidly with multiple threads.
bam files require samtools or sambamba in the path.
Usage: streamsam.sh in=<file> out=<file>
Filtering parameters:
minpos= Ignore alignments not overlapping this range.
maxpos= Ignore alignments not overlapping this range.
minmapq= Ignore alignments with mapq below this.
maxmapq= Ignore alignments with mapq above this.
contigs= Comma-delimited list of contig names to include. These
should have no spaces, or underscores instead of spaces.
mapped=t Include mapped reads.
unmapped=t Include unmapped reads.
secondary=f Include secondary alignments.
supplimentary=t Include supplimentary alignments.
lengthzero=f Include alignments without bases.
invert=f Invert sam filters.
ordered=t Keep reads in input order. False is faster.
ref=<file> Optional reference file.
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="-Xmx1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
streamsam() {
local CMD="java $EA $EOOM $z -cp $CP stream.SamStreamerWrapper $@"
echo $CMD >&2
eval $CMD
}
streamsam "$@"
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