Remove unused sh

snakecnv/bin/svtyper.sh

-#!/bin/bash
-
-# see http://redsymbol.net/articles/unofficial-bash-strict-mode/
-set -euo pipefail
-
-echo "---"
-echo "Running svtyper.sh $1 $2 $3"
-echo "Starting "`date +%Y-%m-%d`" at "`date +%H:%M:%S`
-echo "---"
-
-svtyper=svtyper
-
-root=/home/faraut/work/CapriSV/src/SVPipeline
-export PATH=$root/bin:$PATH
-PYTHONPATH=""
-
-myname=`basename "$0"`
-
-function usage() {
-    echo "
-Program: lumpy wrapper
-usage:   $myname  [options] <bamlist> <input> <outprefix>
-
-positional args:
-        bamlist    a file with the bamfiles
-        input      the input vcf file (gzipped or not)
-        outprefix  prefix of the output file
-        ncpus      the number of cpus, optional [1]
-"
-}
-
-get_bams( ) {
-    bams=""
-    for bamfile in $@; do
-       bams=$bams$bamfile","
-    done
-    bams=${bams%?}
-    echo $bams
-}
-
-function join_by {
-    local IFS="$1";
-    shift;
-    echo "$*"; }
-
-bamlist=${1:-}
-input=${2:-}
-outprefix=${3:-}
-ncpus=${4:-1}   # If parameter is unset or null, the expansion of word is substituted (see https://www.gnu.org/software/bash/manual/bashref.html#Shell-Parameter-Expansion)
-
-if [[ -z ${bamlist} || -z ${input} || -z ${outprefix} ]]
-then
-   usage
-   echo "At least one argument is missing"
-   exit 1
-fi
-
-outprefix=`realpath -s $outprefix`
-
-if [[ ! -s $input ]]
-then
-  echo "$input is not and existing or non empty file.\nExiting!"
-  exit 1
-fi
-input=`realpath -s $input`
-
-bamarray=()
-while read line
-do
-  if [[ ! -s $line ]]
-  then
-    echo "$line is not and existing or non empty file.\nExiting!"
-    exit 1
-  fi
-  path=`realpath -s $line`
-  bamarray+=("$path")
-done < ${bamlist}
-bams=`join_by ',' "${bamarray[@]}"`
-
-origdir=`pwd`
-tempdir=`mktemp -d`
-cd $tempdir
-echo "Working in $tempdir"
-
-# genotype the Structural variants (and parallelize the job)
-awk '{ if( !/^#/) { exit 0; }; print $0}' < <(zless ${input}) > header
-success=1
-zless ${input} | grep -v "^#"  |  split -l 100 - temp_ || success=0
-if [ "${success}" -eq "1" ]; then
-
-for i in temp_*;
-do cat header $i >  $i.raw.vcf
-rm -f $i;done
-ls *.raw.vcf | parallel --no-notice -P ${ncpus} ${svtyper} -i {} -B ${bams} '>' {.}.output
-rm -f lumpy_temp_*.raw.vcf
-vcf-concat *.raw.output | vcf-sort > ${outprefix}.vcf
-
-bgzip -f ${outprefix}.vcf
-tabix -f -p vcf ${outprefix}.vcf.gz
-
-cd $origdir
-rm -fr $tempdir
-
-else
-
-if [ -f ${input} ]; then
-
-cp ${input} ${outprefix}.vcf.gz
-tabix -f -p vcf ${outprefix}.vcf.gz
-
-fi
-
-fi
-
-echo "Script svtyper.sh completed successfully "`date +%Y-%m-%d`" at "`date +%H:%M:%S`