#!/bin/bash
# rundumph5pbc.sh

export SMRT_ROOT=$HOME/bio/pacbio
evigene=$HOME/bio/evigene
bopt="-v --csv --minPredictedAccuracy=70 --minLength=50"

if [ "X" = "X$outdir" ]; then outdir="pbh5out"; echo "WARN: env outdir=$outdir ... default"; fi
if [ "X" = "X$ncpu" ]; then ncpu=15; fi
if [ "X" != "X$opt" ]; then bopt=$opt; fi
if [ "X" = "X$datad" ]; then echo "err missing datad=path/to/data"; exit -1; fi
if [ "X" = "X$indir" ]; then echo "err missing indir=path/to/pacbiohd5dir "; exit -1; fi

export OMP_NUM_THREADS=$ncpu
cd $datad/

if [ -d $indir ]; then
  ls $indir/* > $indir.fofn
  infofn=$indir.fofn
else
  infofn=pbdin$$.fofn
  echo $indir > $infofn
fi


export SMRT_ENV_PASSTHROUGH_VARS="outdir indir ncpu evigene bopt"
source $SMRT_ROOT/current/etc/setup.sh

echo ConsensusTools.sh CircularConsensus $bopt --numThreads=$ncpu --fofn=$infofn -o $outdir --logFile=$outdir.log
ConsensusTools.sh CircularConsensus $bopt --numThreads=$ncpu --fofn=$infofn -o $outdir --logFile=$outdir.log