Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/shred.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| 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 January 13, 2022 | |
| 7 Description: Shreds sequences into shorter, potentially overlapping sequences. | |
| 8 | |
| 9 Usage: shred.sh in=<file> out=<file> length=<number> minlength=<number> overlap=<number> | |
| 10 | |
| 11 in=<file> Input sequences. | |
| 12 out=<file> Destination of output shreds. | |
| 13 length=500 Desired length of shreds. | |
| 14 minlength=1 Shortest allowed shred. The last shred of each input sequence may be shorter than desired length. | |
| 15 overlap=0 Amount of overlap between successive reads. | |
| 16 reads=-1 If nonnegative, stop after this many input sequences. | |
| 17 equal=f Shred each sequence into subsequences of equal size of at most 'length', instead of a fixed size. | |
| 18 median=0 If nonzero, randomly shred reads to a length with this median. | |
| 19 variance=0 If median is nonzero, shred to lengths of median +-variance. | |
| 20 qfake=30 Quality score, if using fastq output. | |
| 21 | |
| 22 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 23 " | |
| 24 } | |
| 25 | |
| 26 #This block allows symlinked shellscripts to correctly set classpath. | |
| 27 pushd . > /dev/null | |
| 28 DIR="${BASH_SOURCE[0]}" | |
| 29 while [ -h "$DIR" ]; do | |
| 30 cd "$(dirname "$DIR")" | |
| 31 DIR="$(readlink "$(basename "$DIR")")" | |
| 32 done | |
| 33 cd "$(dirname "$DIR")" | |
| 34 DIR="$(pwd)/" | |
| 35 popd > /dev/null | |
| 36 | |
| 37 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 38 CP="$DIR""current/" | |
| 39 | |
| 40 z="-Xmx1400m" | |
| 41 set=0 | |
| 42 | |
| 43 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 44 usage | |
| 45 exit | |
| 46 fi | |
| 47 | |
| 48 calcXmx () { | |
| 49 source "$DIR""/calcmem.sh" | |
| 50 setEnvironment | |
| 51 parseXmx "$@" | |
| 52 } | |
| 53 calcXmx "$@" | |
| 54 | |
| 55 stats() { | |
| 56 local CMD="java $EA $EOOM $z -cp $CP jgi.Shred $@" | |
| 57 # echo $CMD >&2 | |
| 58 eval $CMD | |
| 59 } | |
| 60 | |
| 61 stats "$@" |