Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/shuffle.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 November 9, 2016 | |
| 7 | |
| 8 Description: Reorders reads randomly, keeping pairs together. | |
| 9 | |
| 10 Usage: shuffle.sh in=<file> out=<file> | |
| 11 | |
| 12 Standard parameters: | |
| 13 in=<file> The 'in=' flag is needed if the input file is not the first parameter. 'in=stdin' will pipe from standard in. | |
| 14 in2=<file> Use this if 2nd read of pairs are in a different file. | |
| 15 out=<file> The 'out=' flag is needed if the output file is not the second parameter. 'out=stdout' will pipe to standard out. | |
| 16 out2=<file> Use this to write 2nd read of pairs to a different file. | |
| 17 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file. | |
| 18 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster. | |
| 19 int=auto (interleaved) Set to t or f to override interleaving autodetection. | |
| 20 | |
| 21 Processing parameters: | |
| 22 shuffle Randomly reorders reads (default). | |
| 23 name Sort reads by name. | |
| 24 coordinate Sort reads by mapping location. | |
| 25 sequence Sort reads by sequence. | |
| 26 | |
| 27 | |
| 28 Java Parameters: | |
| 29 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 30 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 31 The max is typically 85% of physical memory. | |
| 32 -eoom This flag will cause the process to exit if an out-of-memory | |
| 33 exception occurs. Requires Java 8u92+. | |
| 34 -da Disable assertions. | |
| 35 | |
| 36 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 37 " | |
| 38 } | |
| 39 | |
| 40 #This block allows symlinked shellscripts to correctly set classpath. | |
| 41 pushd . > /dev/null | |
| 42 DIR="${BASH_SOURCE[0]}" | |
| 43 while [ -h "$DIR" ]; do | |
| 44 cd "$(dirname "$DIR")" | |
| 45 DIR="$(readlink "$(basename "$DIR")")" | |
| 46 done | |
| 47 cd "$(dirname "$DIR")" | |
| 48 DIR="$(pwd)/" | |
| 49 popd > /dev/null | |
| 50 | |
| 51 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 52 CP="$DIR""current/" | |
| 53 | |
| 54 z="-Xmx2g" | |
| 55 z2="-Xms2g" | |
| 56 set=0 | |
| 57 | |
| 58 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 59 usage | |
| 60 exit | |
| 61 fi | |
| 62 | |
| 63 calcXmx () { | |
| 64 source "$DIR""/calcmem.sh" | |
| 65 setEnvironment | |
| 66 parseXmx "$@" | |
| 67 if [[ $set == 1 ]]; then | |
| 68 return | |
| 69 fi | |
| 70 freeRam 2000m 84 | |
| 71 z="-Xmx${RAM}m" | |
| 72 z2="-Xms${RAM}m" | |
| 73 } | |
| 74 calcXmx "$@" | |
| 75 | |
| 76 shuffle() { | |
| 77 local CMD="java $EA $EOOM $z $z2 -cp $CP sort.Shuffle $@" | |
| 78 echo $CMD >&2 | |
| 79 eval $CMD | |
| 80 } | |
| 81 | |
| 82 shuffle "$@" |