BAMstat

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

mkdir -p $BAMstatout $BAMstathead
echo "`date +%Y%m%d-%H:%M:%S`: BAM states"

INBAM=$2
INBAMbase=$(basename $INBAM)
OUBAMpre=${BAMstatout}/${INBAMbase/%.bam/}

$SAMTOOLS stat -@ 10 $INBAM > ${OUBAMpre}.stat.txt
$SAMTOOLS flagstat -@ 10 $INBAM > ${OUBAMpre}.flagstat.txt
$SAMTOOLS idxstats -@ 10 $INBAM > ${OUBAMpre}.idxstats.txt
$SAMTOOLS coverage  $INBAM > ${OUBAMpre}.coverage.txt
$PLOTBAMSTATS -p $BAMstathead/${INBAMbase/%.bam/} ${OUBAMpre}.stat.txt

$PRESEQ lc_extrap \
   -output ${OUBAMpre}.ccurve.txt \
   -verbose \
   -bam \
   -pe \
   $INBAM

${JAVA_JDK} -Xmx40g -XX:ParallelGCThreads=20 -jar $PICARD \
    CollectWgsMetrics\
    I=$INBAM \
    O=${OUBAMpre}.CollectWgsMetrics.txt \
    CAP=10000 \
    INCLUDE_BQ_HISTOGRAM=true \
    COUNT_UNPAIRED=true \
    Q=1 \
    REFERENCE_SEQUENCE=$GENOME_REF
#-XX:ConcGCThreads=2

${JAVA_JDK} -Xmx40g -XX:ParallelGCThreads=20 -jar $PICARD \
    CollectInsertSizeMetrics \
    I=$INBAM \
    O=${OUBAMpre}.CollectInsertSizeMetrics.txt \
    H=${OUBAMpre}.CollectInsertSizeMetrics.pdf

<<COMMENT
${JAVA_JDK} -Xmx40g -XX:ParallelGCThreads=20 -jar $PICARD \
   CollectMultipleMetrics \
   I=$INBAM \
   O=${OUBAMpre}.CollectMultipleMetrics.txt \
   REFERENCE_SEQUENCE=$GENOME_REF \
   VALIDATION_STRINGENCY=LENIENT
COMMENT