#!/bin/bash
#run_asd.bash - a helper script that discovers how your stru file is formatted and then runs asd
#    Copyright (C) 2011  Zachary A Szpiech (szpiechz@umich.edu)

#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.

#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.

#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.

EXTRAARGS="--ibs-all --full"
CHECK=1

for i
do
  case "$i" in
        --help) 
	  echo 'Usage: -f <datafile> -s <individual ID column> -t <numthreads> -o';
	  echo 'When -o is present the script will not check if any files will be overwriten';
	  exit 1;;
  esac
done

args=`getopt f:s:t:o $*`
if test $? != 0
     then
         echo 'Usage: -f <datafile> -s <individual ID column> -t <numthreads> -o'
	 echo 'When -o is present the script will not check if any files will be overwriten'
         exit 1
fi
set -- $args
for i
do
    case "$i" in
        -f) shift;FILE=$1;shift;;
        -s) shift;SORT=$1;shift;;
        -t) shift;THREADS=$1;shift;;
	-o) shift;CHECK=0;;
    esac
done

if [ -z $FILE ]
then
    echo "ERROR: Need to provide a data file on argument -f."
    exit
fi

if [ ! -e $FILE ]
then
    echo "ERROR: Could not find $FILE."
    exit
fi

if [ -z $SORT ]
then
    echo "ERROR: Need to provide a non-data column where individual IDs on argument -s."
    exit
fi
if [ -z $THREADS ]
then
    echo "ERROR: Need to provide a number of threads to spawn on argument -t."
    exit
fi

if [[ $SORT != [0-9]* ]]
then
    echo "ERROR: $SORT is not a positive integer.  Please pass a positive integer to -s."
    exit
fi

if [ $SORT -le 0 ]
then
    echo "ERROR: $SORT is not a positive integer.  Please pass a positive integer to -s."
    exit
fi


if [[ $THREADS != [0-9]* ]]
then
    echo "ERROR: $THREADS is not a positive integer.  Please pass a positive integer to -t."
    exit
fi

if [ $THREADS -le 0 ]
then
    echo "ERROR: $THREADS is not a positive integer.  Please pass a positive integer to -t."
    exit
fi

BIN=$(which asd 2> /dev/null)

if [ -z $BIN ]
then
    if [ -e asd ]
    then
	BIN=./asd
    else
	echo "ERROR: Could not find asd in PATH or current directory."
	exit
    fi
fi


for i in head awk wc tail
do
    if [ -z $(which $i 2> /dev/null) ]
    then
	echo "ERROR: Could not find $i in PATH.  You need $i to run this script, and will have to run asd manually."
    fi
done



LOCI=$(head -1 $FILE | awk '{print NF}')

if [[ $LOCI != [0-9]* ]]
then
    echo "ERROR: Found $LOCI loci, which is not a positive integer. Is $FILE empty?"
    exit
else
    echo "Found $LOCI loci."
fi

CURNF=0
NDR=0
NDC=0

until [ $LOCI -lt $CURNF ]
do
    let NDR=$NDR+1
    CURNF=$(head -$NDR $FILE | tail -1 | awk '{print NF}')
    #echo $CURNF
done

let NDR=$NDR-1
let NDC=$CURNF-$LOCI
#let LINES=$(cut -d " " -f1 $FILE | awk 'END{print NR}')-$NDR
let LINES=$(wc -l $FILE | awk '{print $1}')-$NDR

echo "Found $LINES data lines."
echo "Found $NDR header rows."
echo "Found $NDC header columns."

if [ $CHECK -eq 1 ]
then
    for i in .ibs0 .ibs1 .ibs2 .dist
    do
	if [ -e ${FILE}$i ]
	then
	    while [ "$answer" != "Y" ] && [ "$answer" != "n" ]
	    do
		echo -n "WARNING: ${FILE}$i exists already.  Overwrite? (Y/n): "
		read answer
	    done
	    
	    if [ "$answer" == "n" ]
	    then
		echo -n "Rename? (Y/n): "
		while [ "$answer2" != "Y" ] && [ "$answer2" != "n" ]
		do
		    read answer2
		done
		
		if [ "$answer2" == "n" ]
		then
		    echo "Exiting..."
		    exit
		else
		    echo -n "Enter a new name for ${FILE}$i: "
		    read NEWFILENAME
		    mv ${FILE}$i $NEWFILENAME
		    echo "${FILE}$i renamed $NEWFILENAME"
		fi
	    fi
	fi
	
	answer=""
	answer2=""
    done
fi


echo "Running asd with the following parameters:"
echo "$BIN -f $FILE -o $FILE $EXTRAARGS --ndc $NDC --ndr $NDR --threads $THREADS -c $LOCI -r $LINES -s $SORT"

$BIN -f $FILE -o $FILE $EXTRAARGS --ndc $NDC --ndr $NDR --threads $THREADS -c $LOCI -r $LINES -s $SORT