#!/bin/bash

ncpuall=32
ver=2v

export SMRT_ROOT=$HOME/bio/pacbio
evigene=$HOME/bio/evigene
vopt="--verbose"
bopt=""

if [ "X" = "X$outdir" ]; then outdir="pbclassout"; echo "WARN: env outdir=$outdir ... default"; fi
if [ "X" = "X$ncpu" ]; then ncpu=$ncpuall; fi
if [ "X" = "X$datad" ]; then echo "err missing datad=path/to/data"; exit -1; fi
if [ "X" = "X$inlong" ]; then echo "err missing inlong=longreads.fa"; exit -1; fi

export OMP_NUM_THREADS=$ncpu

cd $datad/
inam=`basename $inlong .fasta | sed 's/\.fa$//;'`
ocons=${inam}_cons

if [ "X" != "X$propts" ]; then bopt=$propts; fi
if [ "X" != "X$csize" ]; then bopt="$bopt --cDNA_size $csize"; fi
if [ "X" != "X$infrag" ]; then bopt="$bopt --nfl_fa $infrag"; fi
if [ "X" != "X$inmov" ]; then 
  echo $inmov > $inam.ccs_fofn ;
  bopt="$bopt --ccs_fofn $inam.ccs_fofn"; 
fi


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

copt="--max_sge_jobs 1 --blasr_nproc 4 --quiver_nproc 4"; bopt="$copt $bopt"

echo $SMRT_ROOT/current/analysis/bin/pbtranscript.py $vopt cluster $bopt -d $outdir $inlong $ocons.fa
$SMRT_ROOT/current/analysis/bin/pbtranscript.py $vopt cluster $bopt -d $outdir $inlong $ocons.fa