#!/usr/bin/perl -w
use strict;
use warnings;
use Cwd;

if ($#ARGV < 3 || $#ARGV > 4) {
	die "\nUsage: getresults.pl results_folder output_folder start_range end_range [nproc]";
}

my $input_folder = $ARGV[0];
my $output_folder = $ARGV[1];
my $start = $ARGV[2];
my $end = $ARGV[3];
my $nproc = 1; if ($#ARGV > 3) { $nproc = $ARGV[4]; }

my $count_command = "/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/quake_enhanced/count/count 64";
my $correct_command = "/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/quake_enhanced/test_correction_quality/test_correction_quality";
my $biggenome = "/scratchfast2/snikolenko/ecoli.kmers";
my $cleanup_command = "rm *.part";

my $dir = getcwd;
print $dir . "\n";

sub my_exec {
	my $cmd = shift;
	print $cmd . "\n";
	system $cmd;
}

for (my $i = $start; $i <= $end; ++$i) {
	my $num = sprintf "%02d", $i;
	unless (fork) {
		my_exec("cat $input_folder/$num.reads.left.corrected $input_folder/$num.reads.right.corrected > $input_folder/$num.reads.all.corrected");
		die("$num reads concatenated.");
	}
	my_exec("mkdir $dir/tmpdir$num");
	chdir "$dir/tmpdir$num";
	my_exec("$count_command $input_folder/$num.kmers.solid $input_folder/$num.countkmers.solid 2 500");
	my_exec($cleanup_command);
	my_exec("$count_command $input_folder/$num.kmers.bad $input_folder/$num.countkmers.bad 2 500");
	my_exec($cleanup_command);
	wait(); # cat and previous iteration processes have finished
	my_exec("$count_command $input_folder/$num.reads.all.corrected $input_folder/$num.countkmers.reads 2 500");
	my_exec($cleanup_command);
	chdir "$dir";
	my_exec("rm -rf tmpdir$num");
	# correction can be done in parallel -- it doesn't open 500 files at once
	# besides, we can fire up one new count, so the main process continues along the cycle
	unless (fork) {
		my_exec("$correct_command $biggenome $input_folder/$num.countkmers.solid $input_folder/$num.countkmers.bad > $output_folder/$num.results.solidkmers");
		die("$num solid kmer quality estimated by process $$.");
	}
	unless (fork) {
		my_exec("/home/snikolenko/algorithmic-biology/assembler/build/release/hammer/quake_enhanced/test_correction_quality/test_correction_quality $biggenome $input_folder/$num.countkmers.reads $input_folder/$num.countkmers.bad > $output_folder/$num.results.newreads");
		die("$num reads quality estimated by process $$.");
	}
	if ($$ == 0) { print "Thread 0 done with $num.\n"; }
}
wait();
die("All done.");