Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/vcf2gff.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 August 13, 2019 | |
| 7 | |
| 8 Description: Generates a GFF3 from a VCF. | |
| 9 | |
| 10 Usage: vcf2gff.sh in=<vcf file> out=<gff file> | |
| 11 | |
| 12 Parameters: | |
| 13 in=<file> Input VCF file. | |
| 14 out=<file> Output GFF file. | |
| 15 " | |
| 16 } | |
| 17 | |
| 18 #This block allows symlinked shellscripts to correctly set classpath. | |
| 19 pushd . > /dev/null | |
| 20 DIR="${BASH_SOURCE[0]}" | |
| 21 while [ -h "$DIR" ]; do | |
| 22 cd "$(dirname "$DIR")" | |
| 23 DIR="$(readlink "$(basename "$DIR")")" | |
| 24 done | |
| 25 cd "$(dirname "$DIR")" | |
| 26 DIR="$(pwd)/" | |
| 27 popd > /dev/null | |
| 28 | |
| 29 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 30 CP="$DIR""current/" | |
| 31 | |
| 32 z="-Xmx200m" | |
| 33 set=0 | |
| 34 | |
| 35 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 36 usage | |
| 37 exit | |
| 38 fi | |
| 39 | |
| 40 calcXmx () { | |
| 41 source "$DIR""/calcmem.sh" | |
| 42 setEnvironment | |
| 43 parseXmx "$@" | |
| 44 } | |
| 45 calcXmx "$@" | |
| 46 | |
| 47 gff() { | |
| 48 local CMD="java $EA $EOOM $z -cp $CP gff.GffLine $@" | |
| 49 # echo $CMD >&2 | |
| 50 eval $CMD | |
| 51 } | |
| 52 | |
| 53 gff "$@" |