#!/usr/bin/perl
#$pathname = $ARGV[0];
#**** pathname is inserted here by make_data_dirstruct
$pathname = "xxWORKING_DIRxx";
$datasetname = $ARGV[0];
$fluor_thresh = $ARGV[1];

$cycletable_fn = $pathname."IMAGES/RAW/cycle_id_table.txt";
$baseorderlist_fn = $pathname."EXEC/base_order.dat";
$logfile_fn = $pathname."PROC/DATASETS/create_dataset.log";
print STDERR "Opening logfile $logfile_fn\n";
open LOGFILE, >>$logfile_fn;

#load cycle data into memory
open CYCLETABLE, $cycletable_fn;
$index = 0;
while (<CYCLETABLE>){
    $_ =~ /^([\d]+)\t(.+)\t.+$/g; #input is cycle_num\tcycle_pos\tcycle_type\n ; we ignore the type
    $cycle_num[$index] = $1;
    $cycle_num[$index]++; #we need to convert cycle_num from a string to a number, so we treat it as a number here
    $cycle_num[$index]--;
    $cycle_pos[$index] = $2;
    $index++;
}
$num_cycles = $index;
print LOGFILE "create_dataset.pl executing w/ cycletable $cycletable_fn which has $num_cycles cycles...\n";
print STDERR "create_dataset.pl executing w/ cycletable $cycletable_fn which has $num_cycles cycles...\n";
close CYCLETABLE;

#load base ordering info into memory
open BASEORDERLIST, $baseorderlist_fn;
$index = 0;
while (<BASEORDERLIST>){
    chomp $_;
    $baseorder[$index] = $_;
    print STDERR "$_ ";
    print LOGFILE "$_ ";
    $index++;
}
$num_bases = $index;
print LOGFILE "\n";
print STDERR "\n";
print LOGFILE "create_dataset.pl executing w/ baseorder list $baseorderlist_fn which has $num_bases bases...\n";
print STDERR "create_dataset.pl executing w/ baseorder list $baseorderlist_fn which has $num_bases bases...\n";
close BASEORDERLIST;

#iterate over the number of bases specified in the ordering file, and
#pick the correct cycle numbers from the cycletable
$output_string = "./create_dataset $pathname $datasetname $fluor_thresh 0 ";
for ($i=0; $i<$num_bases; $i++){
    $num_cyc_curr_base = 0;
    $index = 0;
    while ($num_cyc_curr_base < 4){
	if ($index == $num_cycles){
#we couldn't find enough entries for the current position; PROBLEM!
	    print STDERR "ERROR: could not find enough entries for the current position.\n";
	}			       
	if($cycle_pos[$index] eq $baseorder[$i]){
	    $num_cyc_curr_base++;
	    $output_string = $output_string." ".$cycle_num[$index];
	}
	$index++;
    }
}
print "ALL CYCLES PRESENT; EXECUTING:\n$output_string\n";
print LOGFILE "ALL CYCLES PRESENT; EXECUTING:\n$output_string\n";
close LOGFILE;

`$output_string`;