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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified June 16, 2020
Description: Provides some of Reformat's functionality in a ZMW-aware tool.
Usage: reformatpb.sh in=<input file> out=<output file> outb=<bad reads>
File I/O parameters:
in=<file> Primary input.
out=<file> (outgood) Output for good reads.
outb=<file> (outbad) Output for discarded reads.
stats=<file> Print screen output here instead of to the screen.
json=f Print stats as json.
schist=<file> Subread count per ZMW histogram.
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:
kzt=f (keepzmwstogether) Send all reads from a ZMW to the same file,
either good or bad output.
minlen=40 Do not output reads shorter than this, after trimming.
ccsin=f Input reads are CCS, meaning they are all full-pass.
Not currently used for anything.
trimpolya=f Trim terminal poly-A and poly-T sequences, for some isoseq
libraries.
minpolymer=5 Don't trim poly-A sequence shorter than this.
polyerror=0.2 Max error rate for trimming poly-A.
flaglongreads=f True to flag reads longer than 1.5x median to be discarded.
longreadmult=1.5 Multiplier to consider a read suspiciously long.
Whitelists and Blacklists:
whitelist= ZMW identifiers, as a comma-delimited list of integers,
or files with one integer per line. All ZMWs not in the
list will be discarded.
blacklist= All ZMWs in the list will be discarded.
Sampling parameters (avoid using more than one of these at a time):
reads=-1 If positive, quit after processing this many reads.
zmws=-1 If positive, quit after processing this many ZMWs.
bestpass=f Set to true to keep only the best read per ZMW. This is
the median length read of the non-outermost reads.
If there are 2 or fewer passes, the longest will be chosen.
longestpass=f Set to true to keep only the longest read per ZMW.
samplerate=1.0 Retain this fraction of input reads.
samplereadstarget=-1 If positive, retain this many reads.
samplebasestarget=-1 If positive, retain this many bases.
samplezmwstarget=-1 If positive, retain this many ZMWs.
subsamplefromends=f If true, eliminate outermost reads first, then inner.
CCS Parameters (Note: CCS is still experimental)
ccs=f Make a single consensus read per ZMW (CPU-intensive).
minpasses=0 Discard ZMWs with fewer than this many passes (estimated;
first and last subread are usually partial).
minsubreads=0 Discard ZMWs with fewer than this many subreads.
reorient=f Try aligning both strands in case ZMW ordering is broken.
minshredid=0.6 Do not include shreds with identity below this in consensus.
Entropy parameters (recommended setting is 'entropy=t'):
minentropy=-1 Set to 0.4 or above to remove low-entropy reads;
range is 0-1, recommended value is 0.55. 0.7 is too high.
Negative numbers disable this function.
entropyk=3 Kmer length for entropy calculation.
entropylen=350 Reads with entropy below cutoff for at least this many
consecutive bases will be removed.
entropyfraction=0.5 Alternative minimum length for short reads; the shorter
of entropylen and entfraction*readlength will be used.
entropywindow=50 Window size used for entropy calculation.
maxmonomerfraction=0.74 (mmf) Also require this fraction of bases in each
window to be the same base.
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/"
JNI="-Djava.library.path=""$DIR""jni/"
#JNI=""
z="-Xmx2g"
z2="-Xms2g"
#z3="-Xss16m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 2000m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
reformatpb() {
local CMD="java $EA $EOOM $z $z2 -cp $CP icecream.ReformatPacBio $@"
if [[ $silent != 1 ]]; then
echo $CMD >&2
fi
eval $CMD
}
reformatpb "$@"
|
