haplotyper-battle-royale/modules/viquas/viquas

#!/bin/sh
USAGE="
  USAGE:
    viquas reference.fsa reads.bam [o r perform_richness diversity_region_length]
"

NUM_ARGS=$#
case $NUM_ARGS in
  2)
  ;;
  6)
  ;;
  *)
  echo "${USAGE}"
  echo "Incorrect number of arguments: expecting 2 or 6"
  exit 1
esac

if [ ! -f "${1}" ]; then
  echo "Error: ${1} is not a file"
  exit 1
fi

if [ ! -f "${2}" ]; then
  echo "Error: ${2} is not a file"
  exit 1
fi

REFERENCE_FILE=$(basename "${1}")
BAM_FILE=$(basename "${2}")

cp -r /viquas/viquas_files .
cp /viquas/ViQuaS.R .

case $NUM_ARGS in
  2)
    Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}"
  ;;
  6)
    Rscript ./ViQuaS.R "${REFERENCE_FILE}" "${BAM_FILE}" "${@[3:]}"
  ;;
  *)
  echo "${USAGE}"
  echo "Incorrect number of arguments: expecting 2 or 6"
  exit 1
esac

rm -rf ./viquas_files
rm ViQuaS.R