BIGWIG

. $1
. $(dirname $(realpath $0))/env.Configure
. $(dirname $(realpath $0))/env.Variable

mkdir -p $BIGWIGout
echo "`date +%Y%m%d-%H:%M:%S`: Read depth normalised bigWig"

INBAM=$2

#INBAMbase=$(basename $INBAM)
#OUTpre=${BIGWIGout}/${INBAMbase/%.bam/}W
#FLAGstat=$BAMstatout/${INBAMbase/%.bam/}.flagstat.txt
#RPMScale=\$(grep 'mapped (' $FLAGstat | awk '{print 1000000/\$1}')
#cut -f 1,2 ${fasta}.fai > ${fasta}.sizes

TmpScale=$(bc <<< "scale=6;1000000/$($SAMTOOLS view -@ 5 -f 0 -c $INBAM)")
$GENOMECOVERAGEBED \
    -ibam $INBAM \
    -scale $TmpScale \
    -bg -pc | \
    sort -T '.' -k1,1 -k2,2n \
    > ${BIGWIGpre}.scaled.bedGraph

$GENOMECOVERAGEBED \
    -ibam $INBAM \
    -bg -pc | \
    sort -T '.' -k1,1 -k2,2n \
    > ${BIGWIGpre}.deflaut.bedGraph

$BEDGRAPHTOBIGWIG ${BIGWIGpre}.scaled.bedGraph ${GENOME_REF}.fai ${BIGWIGpre}.scaled.bigWig
find $BIGWIGout -type f -name "*.bigWig" -exec echo -e {}"\t0,0,178" \; > ${BIGWIGpre}.bigWig.igv.txt