--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/callvariants.sh	Tue Mar 18 17:55:14 2025 -0400
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+#!/bin/bash
+
+usage(){
+echo "
+Written by Brian Bushnell
+Last modified October 6, 2020
+
+Description:  Calls variants from sam or bam input.
+In default mode, all input files are combined and treated as a single sample.
+In multisample mode, each file is treated as an individual sample,
+and gets its own column in the VCF file.  Unless overridden, input file
+names are used as sample names.
+Please read bbmap/docs/guides/CallVariantsGuide.txt for more information,
+or bbmap/pipelines/variantPipeline.sh for a usage example.
+
+Usage:  callvariants.sh in=<file,file,...> ref=<file> vcf=<file>
+
+Input may be sorted or unsorted.
+The reference should be fasta.
+
+I/O parameters:
+in=<file>       Input; may be one file or multiple comma-delimited files.
+list=<file>     Optional text file containing one input file per line.
+                Use list or in, but not both.
+out=<file>      Output variant list in var format.  If the name ends
+                with .vcf then it will be vcf format.
+vcf=<file>      Output variant list in vcf format.
+outgff=<file>   Output variant list in gff format.
+ref=<file>      Reference fasta.  Required to display ref alleles.
+                Variant calling wil be more accurate with the reference.
+vcfin=<file>    Force calls at these locations, even if allele count is 0.
+shist=<file>    (scorehist) Output for variant score histogram.
+zhist=<file>    (zygosityhist) Output for zygosity histogram.
+qhist=<file>    (qualityhist) Output for variant base quality histogram.
+overwrite=f     (ow) Set to false to force the program to abort rather than
+                overwrite an existing file.
+extended=t      Print additional variant statistics columns.
+sample=         Optional comma-delimited list of sample names.
+multisample=f   (multi) Set to true if there are multiple sam/bam files,
+                and each should be tracked as an individual sample.
+vcf0=           Optional comma-delimited list of per-sample outputs.
+                Only used in multisample mode.
+bgzip=t         Use bgzip for gzip compression.
+samstreamer=t   (ss) Load reads multithreaded to increase speed.
+                Disable to reduce the number of threads used.  The number of
+                streamer threads can be set with e.g. 'ss=4'; default is 6.
+streamermf=8    (ssmf) Allow multiple sam files to be read simultaneously.
+                Set ssmf=X to specify the maximum number or ssmf=f
+                to disable.
+
+Processing Parameters:
+prefilter=f     Use a Bloom filter to exclude variants seen fewer than
+                minreads times.  Doubles the runtime but greatly reduces
+                memory usage.  The results are identical.
+coverage=t      (cc) Calculate coverage, to better call variants.
+ploidy=1        Set the organism's ploidy.
+rarity=1.0      Penalize the quality of variants with allele fraction 
+                lower than this.  For example, if you are interested in
+                4% frequency variants, you could set both rarity and
+                minallelefraction to 0.04.  This is affected by ploidy - 
+                a variant with frequency indicating at least one copy
+                is never penalized.
+covpenalty=0.8  (lowcoveragepenalty) A lower penalty will increase the 
+                scores of low-coverage variants, and is useful for 
+                low-coverage datasets.
+useidentity=t   Include average read identity in score calculation.
+usepairing=t    Include pairing rate in score calculation.
+usebias=t       Include strand bias in score calculation.
+useedist=t      Include read-end distance in score calculation.
+homopolymer=t   Penalize scores of substitutions matching adjacent bases.
+nscan=t         Consider the distance of a variant from contig ends when 
+                calculating strand bias.
+callsub=t       Call substitutions.
+calldel=t       Call deletions.
+callins=t       Call insertions.
+calljunct=f     Call junctions (in development).
+nopassdot=f     Use . as genotype for variations failing the filter.
+
+Coverage Parameters (these mainly affect speed and memory use):
+32bit=f         Set to true to allow coverage tracking over depth 65535,
+                which increases memory use.  Variant calls are impacted
+                where coverage exceeds the maximum.
+atomic=auto     Increases multithreaded speed; forces 32bit to true.
+                Defaults to true if there are more than 8 threads.
+strandedcov=f   (stranded) Tracks per-strand ref coverage to print the MCOV
+                and DP4 fields.  Requires more memory when enabled.  Strand
+                of variant reads is tracked regardless of this flag.
+
+Trimming Parameters:
+border=5        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:
+realign=f       Realign all reads with more than a couple mismatches.
+                Decreases speed.  Recommended for aligners other than BBMap.
+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.
+duplicate=f     Include reads flagged as duplicates.
+invert=f        Invert sam filters.
+
+Variant-Calling Cutoffs:
+minreads=2              (minad) Ignore variants seen in fewer reads.
+maxreads=BIG            (maxad) Ignore variants seen in more reads.
+mincov=0                Ignore variants in lower-coverage locations.
+maxcov=BIG              Ignore variants in higher-coverage locations.
+minqualitymax=15        Ignore variants with lower max base quality.
+minedistmax=20          Ignore variants with lower max distance from read ends.
+minmapqmax=0            Ignore variants with lower max mapq.
+minidmax=0              Ignore variants with lower max read identity.
+minpairingrate=0.1      Ignore variants with lower pairing rate.
+minstrandratio=0.1      Ignore variants with lower plus/minus strand ratio.
+minquality=12.0         Ignore variants with lower average base quality.
+minedist=10.0           Ignore variants with lower average distance from ends.
+minavgmapq=0.0          Ignore variants with lower average mapq.
+minallelefraction=0.1   Ignore variants with lower allele fraction.  This
+                        should be adjusted for high ploidies.
+minid=0                 Ignore variants with lower average read identity.
+minscore=20.0           Ignore variants with lower Phred-scaled score.
+clearfilters            Clear all filters.  Filter flags placed after
+                        the clearfilters flag will still be applied.
+
+There are additionally max filters for score, quality, mapq, allelefraction,
+and identity.
+
+Other Parameters:
+minvarcopies=0          If set to 0, a genotype (vcf GT field) of 0 or 0/0
+                        will be called if observed allele frequency suggests
+                        this is a minor allele.  If set to 1, GT field will
+                        contain at least one 1.
+
+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${RAM}m"
+}
+calcXmx "$@"
+
+callvariants() {
+	local CMD="java $EA $EOOM $z $z2 -cp $CP var2.CallVariants $@"
+	echo $CMD >&2
+	eval $CMD
+}
+
+callvariants "$@"