New upstream version 38.73+dfsg

# Language: Java, Bash

# Information about documentation is in /docs/readme.txt.

# Version 38.62

# Version 38.73

Last modified July 31, 2019

Description:  Does nothing.  Should be fast.

This is a template for making wrappers for new tools.

Usage:  a_sample_mt.sh in=<input file> out=<output file>

Written by Brian Bushnell

Last modified February 17, 2015

***DEPRECATED***

Description:  Randomly adds adapters to a file, or grades a trimmed file.

The input is a set of reads, paired or unpaired.

The output is those same reads with adapter sequence replacing some of the bases in some reads.

#!/bin/bash

usage(){

echo "

Written by Brian Bushnell

Last modified August 22, 2019

Description:  Adds SSU sequence to already-made sketches with TaxIDs.

Usage:           addssu.sh in=a.sketch out=b.sketch ssufile=ssu.fa

Standard parameters:

in=<file>       Input sketch file.

out=<file>      Output sketch file.

ssufile=<file>  A fasta file of SSU sequences.  These should be renamed

                so that they start with tid|# where # is the taxID.

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.

-da             Disable assertions.

For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.

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 3200m 84

	#z="-Xmx${RAM}m"

	#z2="-Xms${RAM}m"

}

calcXmx "$@"

sendsketch() {

	local CMD="java $EA $EOOM $z -cp $CP sketch.AddSSU $@"

	echo $CMD >&2

	eval $CMD

}

sendsketch "$@"

#!/bin/bash

usage(){

echo "

Written by Brian Bushnell

Last modified October 3, 2019

Description:  Shrinks or expands homopolymers.

Usage:  adjusthomopolymers.sh in=<input file> out=<output file> rate=<float>

Input may be fasta or fastq, compressed or uncompressed.

Standard parameters:

in=<file>       Primary input, or read 1 input.

in2=<file>      Read 2 input if reads are in two files.

out=<file>      Primary output, or read 1 output.

out2=<file>     Read 2 output if reads are in two files.

overwrite=f     (ow) Set to false to force the program to abort rather than

                overwrite an existing file.

ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression

                level; lower compression is faster.

Processing parameters:

rate=0.0        0.1 will expand by 10%; -0.1 will shrink by 10%.

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"

z2="-Xms1g"

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 1000m 30

	z="-Xmx${RAM}m"

	z2="-Xms${RAM}m"

}

calcXmx "$@"

adjusthomopolymers() {

	local CMD="java $EA $EOOM $z -cp $CP jgi.AdjustHomopolymers $@"

	echo $CMD >&2

	eval $CMD

}

adjusthomopolymers "$@"