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