#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified September 28, 2023

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.
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:

Sampling parameters:
reads=-1            Set to a positive number to only process this many INPUT reads (or pairs), then quit.

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 "$@"
