#!/bin/ksh

umask 002

case $(uname -s) in

"Linux") 
	   VERSION=staden-1-7-0    #gap4.12

	   . /opt/staden/staden.profile
		;;
"SunOS" )	
	   VERSION=staden-1-7-0    #gap4.12

	   LD_LIBRARY_PATH=/gen/fly/biosw/$VERSION/lib/solaris-binaries:$LD_LIBRARY_PATH
	   export LD_LIBRARY_PATH

	   PATH=/gen/fly/biosw/$VERSION/solaris-bin:$PATH
	   export PATH

	   STADENROOT=/gen/fly/biosw/$VERSION
	   export STADENROOT

	   STADTABL=/gen/fly/biosw/$VERSION/tables
	   export STADTABL

	   STADLIB=/gen/fly/biosw/$VERSION/lib
	   export STADLIB

		;;
"*" )
		echo "unsupported OS"
		exit 1
esac

echo "STADENROOT=$STADENROOT"
echo "PATH=$PATH"

#RPATH=/gen/fly/biosw/roche454ace2gap
#RPATH=$HOME/ace/bin
RPATH=/usr/local/roche2gap/bin
export RPATH

echo "====="
echo "STADENROOT=$STADENROOT"
echo "PATH=$PATH"
echo "RPATH=$RPATH"
echo "====="

SRC=`pwd`
DST=`pwd`
PRJ=
VER=
CUT=5


function usage
{
 printf "\n"
 printf "Usage: %s: [-h, -? ] [-c cutoff ] [ -s SRC ] [ -d DST ]  -p PRO -v VER\n" $0
 printf "\n"
 printf "       -c   reads shorter 'cutoff' skipped; default 5\n"
 printf "\n"
 printf "       -s   source directory;               default HERE\n"
 printf "\n"
 printf "       -d   destination directory,          default HERE\n"
 printf "            contains 454Contigs.ace and folder sff/[A-Z]*.sff\n"
 printf "\n"
 printf "       -p   GAP4 database name,             no defaults\n"
 printf "       -v   GAP4 database version,          no defaults\n"
 printf "       -h   this help\n"
 printf "\n"
 printf "       Example:\n"
 printf "       cd /gen/fox/pro/gs20/Onoda/tmp\n"
 printf "       %s -c 5 -d ../gap4 -p HKI -v 0\n\n" $0
 printf "\n"
 exit 1
}

while getopts hc:s:d:p:v: arg
do
	case $arg in
	c)  CUT=$OPTARG;;
	s)  SRC=$OPTARG;;
	d)  DST=$OPTARG;;
	p)  PRJ=$OPTARG;;
	v)  VER=$OPTARG;;
	h|?) usage;;		 
   esac
done

if [ x"$PRJ" == x ]
then
	echo "\nNo Project given ?"
	usage;
fi

if [ x"$VER" == x ]
then
	echo "\nNo Version given ?"
	usage;
fi
#-------------------
# some simple checks
#-------------------

echo ""
echo "Check DST=$DST ..."

mkdir -p "$DST"

if [ ! -d $DST ]
then
	echo " DST=$DST does not exist"
	exit 1
fi
DST=$(\cd $DST && pwd -P )

echo "Check PRJ=$DST/$PRJ.$VER ..."
if [ -f $DST/$PRJ.$VER -o -f $DST/$PRJ.$VER.aux ]
then
	echo "GAP4 already exist:"
	echo "   $DST/$PRJ.$VER (.aux)"
	exit 1
fi

SRC=$(\cd $SRC && pwd -P )

echo "Check SRC=$SRC/454Contigs.ace ..."
if [ ! -f "$SRC"/454Contigs.ace ]
then
	echo "File "$SRC"/454Contigs.ace missing"
	exit 1
fi
echo "Check SRC=$SRC/454Contigs.qry ..."
if [ -f "$SRC"/454Contigs.qry ]
then
	echo "          $SRC/454Contigs.qry exist;"
fi
echo "Check SRC=$SRC/454Contigs.aln ..."
if [ -f "$SRC"/454Contigs.aln ]
then
	echo "          $SRC/454Contigs.aln exist;"
fi

cd $SRC
echo "Check SRC=$SRC/[A-Z]xxxxxxx.sff ..."

typeset -i i=0
for f in $(ls [A-Z]*.sff 2>/dev/null| grep -v hash)

do 
	i=$((i+1))
done

if [ $i -eq 0 ]
then
	echo "WARN - No such files '*.sff'"
	#exit 1
fi

#----------------
# OK - lets do it
#----------------

echo ""
typeset -i i=0
for f in $(ls [A-Z]*.sff 2>/dev/null| grep -v hash)
do 
	F=${f%.sff}  
    echo "$RPATH/sff_dump -f $F.fna -q $F.qual $f"
	if [ ! -f $F.fna -o ! -f $F.qual ]
	then
    	$RPATH/sff_dump -f $F.fna -q $F.qual $f
	else
		echo "  * Use existing $F.fna and $F.qual"
	fi
	i=$((i+1))
done

echo ""
echo "cd $DST"
for f in $(ls $SRC/[A-Z]*.sff 2>/dev/null | grep -v hash)
do 
    F=${f%%.sff}
	F=${F##*/}
    echo "hash_sff -o $DST/${F}_hash.sff $f"
	if [ ! -f $DST/${F}_hash.sff ]
	then
    	hash_sff -o $DST/${F}_hash.sff $f >/dev/null
	else
		:
		echo "  * Use existing $DST/sff/${F}_hash.sff"
	fi
done


echo ""
echo "cd $SRC"
echo "$RPATH/roche454ace2caf.pl -f 454Contigs.ace -c $CUT > $DST/$PRJ.caf"
      $RPATH/roche454ace2caf.pl -f 454Contigs.ace -c $CUT 2>&1 >$DST/$PRJ.caf  | tee $DST/$PRJ.err

echo ""
echo "cd $DST"
cd $DST

echo "$PWD"
echo "Create GAP4 ..."
echo "$RPATH/caf2gap -project $PRJ -version $VER < $PRJ.caf"
 
$RPATH/caf2gap -silent -project $PRJ -version $VER < $PRJ.caf >/dev/null 2>/dev/null 


#
# chmod - access modification for group
# CAF2GAP creates all project names with uppercase
#
# 
NPRJ=`echo $PRJ | tr 'abcdefghijklmnopqrstuvwxyz' 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'`

mv $NPRJ.$VER      $PRJ.$VER      2>/dev/null
mv $NPRJ.$VER.aux  $PRJ.$VER.aux  2>/dev/null

chmod 664 $PRJ.$VER $PRJ.$VER.aux

cp $RPATH/gap4sff $DST

echo "Cleaning up ..."
#rm -f $SRC/E*.fna
#rm -f $SRC/E*.qual
#rm -f $SRC/454Contigs.qry
#rm -f $SRC/454Contigs.aln
#rm -f $DST/$PRJ.caf

echo ""
echo "Finished;"
echo ""
echo "  cd $DST"
echo "  ./gap4sff $PRJ.$VER"
echo ""