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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified November 8, 2018
Description: Realigns mapped reads to a reference.
Usage: bbrealign.sh in=<file> ref=<file> out=<file>
Input may be a sorted or unsorted sam or bam file.
The reference should be fasta.
I/O parameters:
in=<file> Input reads.
out=<file> Output reads.
ref=<file> Reference fasta.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Trimming parameters:
border=0 Trim at least this many bases on both ends of reads.
qtrim=r Quality-trim reads on this end
r: right, l: left, rl: both, f: don't quality-trim.
trimq=10 Quality-trim bases below this score.
Realignment parameters:
unclip=f Convert clip symbols from exceeding the ends of the
realignment zone into matches and substitutitions.
repadding=70 Pad alignment by this much on each end. Typically,
longer is more accurate for long indels, but greatly
reduces speed.
rerows=602 Use this many rows maximum for realignment. Reads longer
than this cannot be realigned.
recols=2000 Reads may not be aligned to reference seqments longer
than this. Needs to be at least read length plus
max deletion length plus twice padding.
msa= Select the aligner. Options:
MultiStateAligner11ts: Default.
MultiStateAligner9PacBio: Use for PacBio reads, or for
Illumina reads mapped to PacBio/Nanopore reads.
Sam-filtering parameters:
minpos= Ignore alignments not overlapping this range.
maxpos= Ignore alignments not overlapping this range.
minreadmapq=4 Ignore alignments with lower mapq.
contigs= Comma-delimited list of contig names to include. These
should have no spaces, or underscores instead of spaces.
secondary=f Include secondary alignments.
supplimentary=f Include supplimentary alignments.
invert=f Invert sam filters.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
specify 200 megs. The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
bbrealign() {
local CMD="java $EA $EOOM $z $z2 -cp $CP var2.Realign $@"
echo $CMD >&2
eval $CMD
}
bbrealign "$@"
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