Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/removebadbarcodes.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell. | |
| 6 Last modified March 5, 2018 | |
| 7 | |
| 8 Description: Removes reads with barcodes containing non-ACGT bases. | |
| 9 Read headers must be in standard Illumina format. | |
| 10 | |
| 11 Usage: removebadbarcodes.sh in=<file> out=<file> | |
| 12 | |
| 13 Parameters: | |
| 14 in=<file> Input reads; required parameter. | |
| 15 out=<file> Destination for good reads; optional. | |
| 16 ziplevel=2 (zl) Compression level for gzip output. | |
| 17 pigz=f Spawn a pigz (parallel gzip) process for faster | |
| 18 compression than Java. Requires pigz to be installed. | |
| 19 | |
| 20 Java Parameters: | |
| 21 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 22 -Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 megs. | |
| 23 The max is typically 85% of physical memory. | |
| 24 -eoom This flag will cause the process to exit if an out-of-memory | |
| 25 exception occurs. Requires Java 8u92+. | |
| 26 -da Disable assertions. | |
| 27 | |
| 28 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 29 " | |
| 30 } | |
| 31 | |
| 32 #This block allows symlinked shellscripts to correctly set classpath. | |
| 33 pushd . > /dev/null | |
| 34 DIR="${BASH_SOURCE[0]}" | |
| 35 while [ -h "$DIR" ]; do | |
| 36 cd "$(dirname "$DIR")" | |
| 37 DIR="$(readlink "$(basename "$DIR")")" | |
| 38 done | |
| 39 cd "$(dirname "$DIR")" | |
| 40 DIR="$(pwd)/" | |
| 41 popd > /dev/null | |
| 42 | |
| 43 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 44 CP="$DIR""current/" | |
| 45 JNI="-Djava.library.path=""$DIR""jni/" | |
| 46 JNI="" | |
| 47 | |
| 48 z="-Xmx200m" | |
| 49 z2="-Xms200m" | |
| 50 set=0 | |
| 51 | |
| 52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 53 usage | |
| 54 exit | |
| 55 fi | |
| 56 | |
| 57 calcXmx () { | |
| 58 source "$DIR""/calcmem.sh" | |
| 59 setEnvironment | |
| 60 parseXmx "$@" | |
| 61 } | |
| 62 calcXmx "$@" | |
| 63 | |
| 64 | |
| 65 removebadbarcodes() { | |
| 66 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.RemoveBadBarcodes $@" | |
| 67 echo $CMD >&2 | |
| 68 eval $CMD | |
| 69 } | |
| 70 | |
| 71 removebadbarcodes "$@" |