1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
|
#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified May 14, 2024
Description: Counts and summarizes the number of reads with each barcode,
using class BarcodeStats. Can also do barcode assignment.
Usage: countbarcodes.sh in=<file> counts=<file>
Input may be stdin or a fasta or fastq file, raw or gzipped.
Input Parameters:
in=<file> Input reads, whose names end in a colon then barcode.
countsin=<file> Input of counts; optional.
quantset=<file> Only quantify barcodes in this file.
interleaved=auto (int) If true, fastq input will be considered interleaved.
expected= Comma-delimited list of expected bar codes.
Output parameters:
maxrows=-1 Optionally limit the number of rows printed.
printheader=t Print a header.
out=<file> (counts) Write bar codes and counts here. 'out=stdout'
will pipe to standard out.
barcodesout=<file> Barcode assignment counts.
mapout=<file> Map of observed to expected barcode assignments.
outcontam=<file> Requires labeled data, and causes contam quantification.
Processing Parameters:
countundefined=t Count barcodes that contain non-ACGT symbols.
pcrmatrix=f Use a PCRMatrix for barcode assignment.
mode=hdist PCRMatrix type.
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"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
countbarcodes() {
local CMD="java $EA $EOOM $z -cp $CP barcode.CountBarcodes2 $@"
echo $CMD >&2
eval $CMD
}
countbarcodes "$@"
|
