--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/demuxbyname.sh	Tue Mar 18 17:55:14 2025 -0400
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+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified Jan 7, 2020
+
+Description:  Demultiplexes sequences into multiple files based on their names,
+substrings of their names, or prefixes or suffixes of their names.
+Allows unlimited output files while maintaining only a small number of open file handles.
+
+Usage:
+demuxbyname.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> names=<string,string,string...>
+
+Alternately:
+demuxbyname.sh in=<file> out=<outfile> delimiter=whitespace prefixmode=f
+This will demultiplex by the substring after the last whitespace.
+
+demuxbyname.sh in=<file> out=<outfile> length=8 prefixmode=t
+This will demultiplex by the first 8 characters of read names.
+
+demuxbyname.sh in=<file> out=<outfile> delimiter=: prefixmode=f
+This will split on colons, and use the last substring as the name; useful for
+demuxing by barcode for Illumina headers in this format:
+@A00178:73:HH7H3DSXX:4:1101:13666:1047 1:N:0:ACGTTGGT+TGACGCAT
+
+in2 and out2 are for paired reads in twin files and are optional.
+If input is paired and there is only one output file, it will be written interleaved.
+
+File Parameters:
+in=<file>       Input file.
+in2=<file>      If input reads are paired in twin files, use in2 for the second file.
+out=<file>      Output files for reads with matched headers (must contain % symbol).
+                For example, out=out_%.fq with names XX and YY would create out_XX.fq and out_YY.fq.
+                If twin files for paired reads are desired, use the # symbol.  For example,
+                out=out_%_#.fq in this case would create out_XX_1.fq, out_XX_2.fq, out_YY_1.fq, etc.
+outu=<file>     Output file for reads with unmatched headers.
+stats=<file>    Print statistics about how many reads went to each file.
+
+Processing Modes (determines how to convert a read into a name):
+prefixmode=t    (pm) Match prefix of read header.  If false, match suffix of read header.
+                prefixmode=f is equivalent to suffixmode=t.
+barcode=f       Parse barcodes from Illumina headers.
+chrom=f         For mapped sam files, make one file per chromosome (scaffold) using the rname.
+header=f        Use the entire sequence header.
+delimiter=      For prefix or suffix mode, specifying a delimiter will allow exact matches even if the length is variable.
+                This allows demultiplexing based on names that are found without specifying a list of names.
+                In suffix mode, for example, everything after the last delimiter will be used.
+                Normally the delimiter will be used as a literal string (a Java regular expression); for example, ':' or 'HISEQ'.
+                But there are some special delimiters which will be replaced by the symbol they name, 
+                because they are reserved in some operating systems or cause other problems.
+                These are provided for convenience due to possible OS conflicts:
+                   space, tab, whitespace, pound, greaterthan, lessthan, equals,
+                   colon, semicolon, bang, and, quote, singlequote
+                These are provided because they interfere with Java regular expression syntax:
+                   backslash, hat, dollar, dot, pipe, questionmark, star,
+                   plus, openparen, closeparen, opensquare, opencurly
+                In other words, to match '.', you should set 'delimiter=dot'.
+substring=f     Names can be substrings of read headers.  Substring mode is
+                slow if the list of names is large.  Requires a list of names.
+
+Other Processing Parameters:
+column=-1       If positive, split the header on a delimiter and match that column (1-based).
+                For example, using this header:
+                NB501886:61:HL3GMAFXX:1:11101:10717:1140 1:N:0:ACTGAGC+ATTAGAC
+                You could demux by tile (11101) using 'delimiter=: column=5'
+                Column is 1-based (first column is 1).
+                If column is omitted when a delimiter is present, prefixmode
+                will use the first substring, and suffixmode will use the last substring.
+names=          List of strings (or files containing strings) to parse from read names.
+                If the names are in text files, there should be one name per line.
+                This is optional.  If a list of names is provided, files will only be created for those names.
+                For example, 'prefixmode=t length=5' would create a file for every unique last 5 characters in read names,
+                and every read would be written to one of those files.  But if there was addionally 'names=ABCDE,FGHIJ' 
+                then at most 2 files would be created, and anything not matching those names would go to outu.
+length=0        If positive, use a suffix or prefix of this length from read name instead of or in addition to the list of names.
+                For example, you could create files based on the first 8 characters of read names.
+hdist=0         Allow a hamming distance for demultiplexing barcodes.  This requires a list of names (barcodes).
+replace=        Replace some characters in the output filenames.  For example, replace=+-
+                would replace the + symbol in headers with the - symbol in filenames.  So you could
+                match the name ACTGAGC+ATTAGAC in the header, but write to a file named ACTGAGC-ATTAGAC.
+
+Buffering Parameters
+streams=4       Allow at most this many active streams.  The actual number of open files
+                will be 1 greater than this if outu is set, and doubled if output
+                is paired and written in twin files instead of interleaved.
+minreads=0      Don't create a file for fewer than this many reads; instead, send them to unknown.
+                This option will incur additional memory usage.
+
+Common parameters:
+ow=t            (overwrite) Overwrites files that already exist.
+zl=4            (ziplevel) Set compression level, 1 (low) to 9 (max).
+int=auto        (interleaved) Determines whether INPUT file is considered interleaved.
+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).
+                    
+
+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="-Xmx2g"
+z2="-Xms2g"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+	if [[ $set == 1 ]]; then
+	return
+	fi
+	freeRam 3200m 84
+	z="-Xmx${RAM}m"
+	z2="-Xms${RAM}m"
+}
+calcXmx "$@"
+
+function demuxbyname() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.DemuxByName2 $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+demuxbyname "$@"