/\		       /\
			   /  \<-----NO-------/  \<---------------+
			  /    \	     /    \	     +----|----+
 +-------+   +------+	 /  new \	    / new  \	     | process |
 | start |-->| menu |-->< patient>--YES--->< panel  >--YES-->} patient ]
 +-------+   +------+	 \   ?  /	    \  ?   /	     | & panel |
			  \    /    +------+ \    /	     +---------+
       +-------------------\  /-NO->| exit |  \  /-------------------+
       |		    \/      +------+   \/		     |
       |		    ^			^		     |
       |		    |			|		     |
       +--Invalid response--+		    	+--Invalid response--+

#!/bin/bash

# Main menu...
menu() {
	# Loop reading patient IDs; exit on zero or EOF.
	while [ 1 ]
	do	clear
		printf '\n\nEEnter patient ID (0 to exit): '
		if ! read id || [ "$id" = 0 ]
		then	break
		fi
		if [ "$id" = "" ] || [ "$id" != "${id#*[^0-9]}" ]
		then	printf '\nPatiend ID must be numeric; try again.\n'
			sleep 5
			continue
		fi
		process_panels
	done
        printf "\nBye!\n"
	exit
}

# Proess panels for the current patient ID
process_panels() {
	# Loop reading panels to process for current patient ID ($id)...
	while [ 1 ]
	do	printf "\nEnter panel number for patient ID $id (0 when done): "
		if ! read panel || [ "$panel" = 0 ]
		then	return
		fi
		if [ "$panel" = "" ] || [ "$panel" != "${panel#*[^0-9]}" ]
		then	printf '\nPanel number must be numeric; try again\n'
			continue
		fi

		# Process this panel for this patient...
		printf "DEBUG INFO: Processing patient ID $id, panel $panel\n"
		$(perl -aF/\\t/ -lne 'BEGIN{%m=map{chomp
			s/\cM|\cJ//g
			$p=join("\t",(split/\t/)[4,5])
			($p,$_)} <>
			$m{"#CHROM\tINFO"}=$m{"Chr\tSegment Position"}}
			/SEGPOS=(\d+)/ || /\t(INFO)\t/ or next
			$p=$F[0]."\t".$1
			exists $m{$p} and print join("\t",$_,$m{$p})' \
			${id}_${panel}_${OMR}.txt \
			< ${id}_${panel}_${OMR}_Filtered.vcf \
			> ${id}_matched.vcf)
		printf "\nConvert patient ID $id, panel $panel file (Y/N)?: "
		read convert_choice
		case "$convert_choice" in
		([yY])	printf "Converting patient ID $id, panel $panel file.\n"
			$ perl convert2annovar.pl -includeinfo \
				-format vcf4old ${id}_matched.vcf \
				> ${id}_matched.avinput)
		esac
	done
}

# Initialize location and variables...
cd 'C:\Users\cmccabe\Desktop\annovar'
OMR=Output_Mutation_Report

# Loop through user supplied patient IDs and loop though panels for each
# patient...
menu