applyFilter.sh

#!/bin/bash

SDIR="$( cd "$( dirname "$0" )" && pwd )"

if [ -x "$(command -v git)" ] && [ -r "$SDIR/.git" ]
then
    # if both Git CLI and .git exist, then use "git describe" to create version tag
    SVERSION=$(git --git-dir=$SDIR/.git --work-tree=$SDIR describe --tags)
else
    if [ -r "${SDIR}/.git-commit-hash" ]
    then
        # if .git-commit-hash exists, then use the git commit hash stored in .git-commit-hash
        SVERSION=$(cat ${SDIR}/.git-commit-hash)
    else
        # if we can't figure it out, use a hardcoded version number that we need to keep updated
        SVERSION="v1.2.1"
    fi
fi

# construct version tag
VTAG="$(basename $SDIR)/$(basename $0) VERSION=$SVERSION"

usage() {
    echo "applyFilter.sh FILTER_SCRIPT IN_MAF OUT_MAF [Additional parameters for Filter]"
    echo
    echo "    Run the filter (FILTER_SCRIPT) on the input maf and"
    echo "    write a properly headered output maf"
    echo
    echo "    If the filter script require more parameters they"
    echo "    can be passed after the output maf name"
    echo ""
    echo "  "$VTAG
    echo
    exit
}

if [ "$#" -lt "3" ]; then
    usage
fi

FILTER=$1
MAFIN=$2
MAFOUT=$3

shift 3

# Resolve filter to full path
FILTER=$SDIR/$(basename $FILTER)
if [ ! -e $FILTER ]; then
    echo "ERROR: Non-existant filter" $(basename $FILTER)
    exit 1
fi

#
# Check if MAF has proper version header
# If not add it.
#

HEADER=$(head -1 $MAFIN)
if [[ ! "$HEADER" =~ ^# ]]; then
    echo "#version 2.4" > $MAFOUT
else
    egrep "^#" $MAFIN > $MAFOUT
fi

# Add version tag

echo "#$VTAG FILTER=$(basename $FILTER)" >>$MAFOUT

TMPMAF=$(uuidgen).maf


Rscript --vanilla  $FILTER -m $MAFIN -o $TMPMAF $*
EXIT_CODE=$?

if [ "$EXIT_CODE" != "0" ]; then
    echo "ERROR IN R-script"
    exit 1
fi


cat $TMPMAF >>$MAFOUT
rm $TMPMAF