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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 25, 2024
Description: Renames reads to <prefix>_<number> where you specify the prefix
and the numbers are ordered. There are other renaming modes too.
If reads are paired, pairs should be processed together; if reads are
interleaved, the interleaved flag should be set. This ensures that if a
read number (such as 1: or 2:) is added, it will be added correctly.
Usage: rename.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> prefix=<>
in2 and out2 are for paired reads and are optional.
If input is paired and there is only one output file, it will be written interleaved.
Parameters:
prefix= The string to prepend to existing read names.
suffix= If a suffix is supplied, it will be appended to the existing read name, after a tab.
ow=f (overwrite) Overwrites files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
fastawrap=70 Length of lines in fasta output.
minscaf=1 Ignore fasta reads shorter than this.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
ignorebadquality=f (ibq) Fix out-of-range quality values instead of crashing with a warning.
Renaming modes (if not default):
renamebyinsert=f Rename the read to indicate its correct insert size.
renamebymapping=f Rename the read to indicate its correct mapping coordinates.
renamebytrim=f Rename the read to indicate its correct post-trimming length.
renamebycoords=f Rename Illumina headers to leave coordinates but remove redundant info.
addprefix=f Rename the read by prepending the prefix to the existing name.
prefixonly=f Only use the prefix; don't add _<number>
addunderscore=t Add an underscore after the prefix (if there is a prefix).
addpairnum=t Add a pairnum (e.g. ' 1:') to paired reads in some modes.
fixsra=f Fixes headers of SRA reads renamed from Illumina.
Specifically, it converts something like this:
SRR17611.11 HWI-ST79:17:D091UACXX:4:1101:210:824 length=75
...into this:
HWI-ST79:17:D091UACXX:4:1101:210:824 1:
Trimming:
trimleft=0 Trim this many characters from the header start.
trimright=0 Trim this many characters from the header end.
trimbeforesymbol=0 Trim this many characters before the last instance of
a specified symbol.
symbol= Trim before this symbol. This can be a literal like ':'
or a word like tab or lessthan for reserved symbols.
Other parameters:
reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
quantize= Set this to reduce compressed file size by binning quality.
E.g., quantize=2 will eliminate odd qscores.
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="-Xmx1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function rename() {
local CMD="java $EA $EOOM $z -cp $CP jgi.RenameReads $@"
echo $CMD >&2
eval $CMD
}
rename "$@"
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