--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/stats.sh	Tue Mar 18 17:55:14 2025 -0400
@@ -0,0 +1,109 @@
+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified March 3, 2020
+
+Description:  Generates basic assembly statistics such as scaffold count, 
+N50, L50, GC content, gap percent, etc.  For multiple files, please use
+statswrapper.sh.  Works with fasta and fastq only (gzipped is fine).
+Please read bbmap/docs/guides/StatsGuide.txt for more information.
+
+Usage:        stats.sh in=<file>
+
+Parameters:
+in=file         Specify the input fasta file, or stdin.
+out=stdout      Destination of primary output; may be directed to a file.
+gc=file         Writes ACGTN content per scaffold to a file.
+gchist=file     Filename to output scaffold gc content histogram.
+shist=file      Filename to output cumulative scaffold length histogram.
+gcbins=200      Number of bins for gc histogram.
+n=10            Number of contiguous Ns to signify a break between contigs.
+k=13            Estimate memory usage of BBMap with this kmer length.
+minscaf=0       Ignore scaffolds shorter than this.
+phs=f           (printheaderstats) Set to true to print total size of headers.
+n90=t           (printn90) Print the N/L90 metrics.
+extended=f      Print additional metrics such as L90, logsum, and score.
+pdl=f           (printduplicatelines) Set to true to print lines in the 
+                scaffold size table where the counts did not change.
+n_=t            This flag will prefix the terms 'contigs' and 'scaffolds'
+                with 'n_' in formats 3-6.
+addname=f       Adds a column for input file name, for formats 3-6.
+
+Logsum and Powsum:
+logoffset=1000  Minimum length for calculating log sum.
+logbase=2       Log base for calculating log sum.
+logpower=1      Raise the log to a power to increase the weight 
+                of longer scaffolds for log sum.
+powsum=0.25     Use this power of the length to increase weight
+                of longer scaffolds for power sum.
+
+Assembly Score Metric:
+score=f         Print assembly score.
+aligned=0.0     Set the fraction of aligned reads (0-1).
+assemblyscoreminlen=2000   Minimum length of scaffolds to include in
+                           assembly score calculation.
+assemblyscoremaxlen=50000  Maximum length of scaffolds to get bonus points
+                           for being long.
+
+
+format=<0-7>    Format of the stats information; default 1.
+	format=0 prints no assembly stats.
+	format=1 uses variable units like MB and KB, and is designed for compatibility with existing tools.
+	format=2 uses only whole numbers of bases, with no commas in numbers, and is designed for machine parsing.
+	format=3 outputs stats in 2 rows of tab-delimited columns: a header row and a data row.
+	format=4 is like 3 but with scaffold data only.
+	format=5 is like 3 but with contig data only.
+	format=6 is like 3 but the header starts with a #.
+	format=7 is like 1 but only prints contig info.
+	format=8 is like 3 but in JSON.  You can also just use the 'json' flag.
+
+gcformat=<0-5>  Select GC output format; default 1.
+	gcformat=0:	(no base content info printed)
+	gcformat=1:	name	length	A	C	G	T	N	GC
+	gcformat=2:	name	GC
+	gcformat=4:	name	length	GC
+	gcformat=5:	name	length	GC	logsum	powsum
+	Note that in gcformat 1, A+C+G+T=1 even when N is nonzero.
+
+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="-Xmx120m"
+set=0
+
+if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
+	usage
+	exit
+fi
+
+calcXmx () {
+	source "$DIR""/calcmem.sh"
+	setEnvironment
+	parseXmx "$@"
+}
+calcXmx "$@"
+
+stats() {
+	local CMD="java $EA $EOOM $z -cp $CP jgi.AssemblyStats2 $@"
+#	echo $CMD >&2
+	eval $CMD
+}
+
+stats "$@"