#!/usr/bin/env perl
#
# Authors: Adam Auton, Petr Danecek
# (C) 2011

use strict;
use warnings;
use Carp;

my $opts = parse_params();
fix_file($opts);

exit;

#--------------------------------

sub error
{
	my (@msg) = @_;
	if ( scalar @msg ) { confess @msg; }
	die
		"About: Reads in a VCF file with any (commonly used) newline representation and outputs with the\n",
		"	current system's newline representation.\n",
		"Usage: vcf-fix-newlines [OPTIONS]\n",
		"Options:\n",
		"   -i, --info                      Report if the file is consistent with the current platform based.\n",
		"   -h, -?, --help                  This help message.\n",
		"Example:\n",
		"	vcf-fix-newlines -i file.vcf\n",
		"	vcf-fix-newlines file.vcf.gz > out.vcf\n",
		"	cat file.vcf | vcf-fix-newlines > out.vcf\n",
		"\n";
}

sub parse_params
{
	my $opts = {};
	while (defined(my $arg=shift(@ARGV)))
	{
		if ( $arg eq '-i' || $arg eq '--info' ) { $$opts{info}=1; next }
		if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
		if ( !exists($$opts{vcf}) && -e $arg ) { $$opts{vcf}=$arg; next; }
		error("Unknown parameter \"$arg\". Run -h for help.\n");
	}
	return $opts;
}

sub fix_file
{
	my ($opts) = @_;

	my $fh = \*STDIN;
	if ( $$opts{vcf} )
	{
		if ( $$opts{vcf}=~/\.gz/i )
		{
			open($fh,"gunzip -c $$opts{vcf} |") or error("gunzip -c $$opts{vcf}: $!\n");
		}
		else
		{
			open($fh,'<',$$opts{vcf}) or error("$$opts{vcf}: $!\n");
		}
	}

	# Read a small 1kb sample
	binmode $fh or error("binmode: $!");
	local $/ = \1024;
	my $buf  = <$fh>;
	if ( !defined $buf ) { error("No data read.\n"); }

	# Check the origin
	my ($in,$nl);
	if ( $buf=~/\015\012/ ) { $in = 'Windows'; $nl=$&; }
	elsif ( $buf=~/\015/ && !($buf=~/\012/) ) { $in = 'Old Mac'; $nl=$&; }
	elsif ( $buf=~/\012/ && !($buf=~/\015/) ) { $in = 'UNIX'; $nl=$&; }
	else
	{
		error("FIXME: Unable to determine the system which produced the file.\n");
	}
	if ( defined $in ) { warn("The file was generated on $in compatible system.\n"); }
	if ( $$opts{info} ) { close($fh); return; }
	if ( $nl eq "\n" ) { warn("No conversion needed.\n"); return; }

	# Read the file and do the conversion
	local $/ = $nl;
	$buf .= <$fh>;
	$buf =~ s/$nl/\n/g;
	print $buf;

	while($buf = <$fh>)
	{
		$buf =~ s/$nl/\n/g;
		print $buf;
	}
	close($fh);
}