centrifuge

#!/usr/bin/env perl

#
# Copyright 2014, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of Centrifuge, which is copied and modified from bowtie2 in
# the Bowtie2 package.
#
# Centrifuge 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.
#
# Centrifuge 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 Centrifuge.  If not, see <http://www.gnu.org/licenses/>.
#

# centrifuge:
#
# A wrapper script for centrifuge.  Provides various advantages over running
# centrifuge directly, including:
#
# 1. Handling compressed inputs
# 2. Redirecting output to various files
# 3. Output directly to bam (not currently supported)

use strict;
use warnings;
use Getopt::Long qw(GetOptions);
use File::Spec;
use POSIX;


my ($vol,$script_path,$prog);
$prog = File::Spec->rel2abs( __FILE__ );

while (-f $prog && -l $prog){
    my (undef, $dir, undef) = File::Spec->splitpath($prog);
    $prog = File::Spec->rel2abs(readlink($prog), $dir);
}

($vol,$script_path,$prog) 
                = File::Spec->splitpath($prog);
my $os_is_nix   = ($^O eq "linux") || ($^O eq "darwin");
my $align_bin_s = $os_is_nix ? 'centrifuge-class' : 'centrifuge-class.exe'; 
my $build_bin   = $os_is_nix ? 'centrifuge-build' : 'centrifuge-build.exe';               
my $align_prog  = File::Spec->catpath($vol,$script_path,'centrifuge-class');
my $idx_ext       = 'hc'; 
my %signo       = ();
my @signame     = ();

{
	# Get signal info
	use Config;
	my $i = 0;
	for my $name (split(' ', $Config{sig_name})) {
		$signo{$name} = $i;
		$signame[$i] = $name;
		$i++;
	}
}

(-x "$align_prog") ||
	Fail("Expected centrifuge to be in same directory with centrifuge-class:\n$script_path\n");

# Get description of arguments from Centrifuge so that we can distinguish Centrifuge
# args from wrapper args
sub getBt2Desc($) {
	my $d = shift;
	my $cmd = "$align_prog --wrapper basic-0 --arg-desc";
	open(my $fh, "$cmd |") || Fail("Failed to run command '$cmd'\n");
	while(readline $fh) {
		chomp;
		next if /^\s*$/;
		my @ts = split(/\t/);
		$d->{$ts[0]} = $ts[1];
	}
	close($fh);
	$? == 0 || Fail("Description of arguments failed!\n");
}

my %desc = ();
my %wrapped = ("1" => 1, "2" => 1);
getBt2Desc(\%desc);

# Given an option like -1, determine whether it's wrapped (i.e. should be
# handled by this script rather than being passed along to Centrifuge)
sub isWrapped($) { return defined($wrapped{$_[0]}); }

my @orig_argv = @ARGV;

my @bt2w_args = (); # options for wrapper
my @bt2_args  = (); # options for Centrifuge
my $saw_dd = 0;
for(0..$#ARGV) {
	if($ARGV[$_] eq "--") {
		$saw_dd = 1;
		next;
	} 
	push @bt2w_args, $ARGV[$_] if !$saw_dd;
	push @bt2_args,  $ARGV[$_] if  $saw_dd;
}
if(!$saw_dd) {
	@bt2_args = @bt2w_args;
	@bt2w_args= ();
}

my $debug = 0;
my %read_fns = ();
my %read_compress = ();
my $cap_out = undef;       # Filename for passthrough
my $no_unal = 0;
my $large_idx = 0;

# Variables handling the output format
my $outputFmtSam = 0 ;
my $tabFmtOptIdx = 0 ;
my $needReadSeq = 0 ;
my $removeSeqCols = 0 ;

# Variable hanlding multiple sample
my $sampleSheetFile = undef ;
my $otherInput = undef ;
my @sampleSheet ;
my @sampleSheetOrder ; # map to the order centrifuge process the samples.

# Remove whitespace
for my $i (0..$#bt2_args) {
	$bt2_args[$i]=~ s/^\s+//; $bt2_args[$i] =~ s/\s+$//;
}

# We've handled arguments that the user has explicitly directed either to the
# wrapper or to centrifuge, now we capture some of the centrifuge arguments that
# ought to be handled in the wrapper
for(my $i = 0; $i < scalar(@bt2_args); $i++) {
	next unless defined($bt2_args[$i]);
	my $arg = $bt2_args[$i];
	my @args = split(/=/, $arg);
	if(scalar(@args) > 2) {
		$args[1] = join("=", @args[1..$#args]);
	}
	$arg = $args[0];

	if ( $arg eq "--sample-sheet" ) {
		$bt2_args[$i] = undef ;
		++$i ;
		$sampleSheetFile = $bt2_args[ $i ] ;
		$bt2_args[$i] = undef ;
	}

	if($arg eq "-U" || $arg eq "--unpaired") {
		$bt2_args[$i] = undef;
		$arg =~ s/^-U//; $arg =~ s/^--unpaired//;
		if($arg ne "") {
			# Argument was part of this token
			my @args = split(/,/, $arg);
			for my $a (@args) { push @bt2w_args, ("-U", $a); }
		} else {
			# Argument is in the next token
			$i < scalar(@bt2_args)-1 || Fail("Argument expected in next token!\n");
			$i++;
			my @args = split(/,/, $bt2_args[$i]);
			for my $a (@args) { push @bt2w_args, ("-U", $a); }
			$bt2_args[$i] = undef;
		}
		$otherInput = 1 ;
	}
	if($arg =~ /^--?([12])/ && $arg !~ /^--?12/) {
		my $mate = $1;
		$bt2_args[$i] = undef;
		$arg =~ s/^--?[12]//;
		if($arg ne "") {
			# Argument was part of this token
			my @args = split(/,/, $arg);
			for my $a (@args) { push @bt2w_args, ("-$mate", $a); }
		} else {
			# Argument is in the next token
			$i < scalar(@bt2_args)-1 || Fail("Argument expected in next token!\n");
			$i++;
			my @args = split(/,/, $bt2_args[$i]);
			for my $a (@args) { push @bt2w_args, ("-$mate", $a); }
			$bt2_args[$i] = undef;
		}
		$otherInput = 1 ;
	}
	if($arg eq "--debug") {
		$debug = 1;
		$bt2_args[$i] = undef;
	}
	if($arg eq "--no-unal") {
		$no_unal = 1;
		$bt2_args[$i] = undef;
	}
	if($arg eq "--large-index") {
		$large_idx = 1;
		$bt2_args[$i] = undef;
	}
  
  if ($arg eq "--temp-directory") {
    push @bt2w_args, $bt2_args[$i] ;
    push @bt2w_args, $bt2_args[$i + 1] ;
    $bt2_args[$i] = undef ;
    $bt2_args[$i + 1] = undef ;
    next ;
  }

	for my $rarg ("un-conc", "al-conc", "un", "al") {
		if($arg =~ /^--${rarg}$/ || $arg =~ /^--${rarg}-gz$/ || $arg =~ /^--${rarg}-bz2$/) {
			$needReadSeq = 1 ;
			$bt2_args[$i] = undef;
			if(scalar(@args) > 1 && $args[1] ne "") {
				$read_fns{$rarg} = $args[1];
			} else {
				$i < scalar(@bt2_args)-1 || Fail("--${rarg}* option takes an argument.\n");
				$read_fns{$rarg} = $bt2_args[$i+1];
				$bt2_args[$i+1] = undef;
			}
			$read_compress{$rarg} = "";
			$read_compress{$rarg} = "gzip"  if $arg eq "--${rarg}-gz";
			$read_compress{$rarg} = "bzip2" if $arg eq "--${rarg}-bz2";
			last;
		}
	}
	if ($arg eq "--out-fmt" )
	{
		$i < scalar(@bt2_args)-1 || Fail("Argument expected in next token!\n");
		$i++;
		if ( $bt2_args[$i] eq "sam" ) 
		{
			$outputFmtSam = 1 ;
		}
		#$bt2_args[$i] = undef;

	}

	if ( $arg eq "--tab-fmt-cols" )
	{
		$i < scalar(@bt2_args)-1 || Fail("Argument expected in next token!\n");
		$tabFmtOptIdx = $i + 1 ;
	}
}

# process the sample sheet
if ( defined $sampleSheetFile )
{
	Fail( "Can not specify other read files by -U,-1,-2 when using --sample-sheet!\n" ) if ( defined $otherInput ) ;
	push @bt2_args, "--separator" ;

	open FP1, $sampleSheetFile or Fail( "Could not open sample sheet file ".$sampleSheetFile."\n" ) ;
	my $singleCnt = 0 ;
	my $mateCnt = 0 ;
	while ( <FP1> )
	{
		chomp ;
		my @cols = split /\t/, $_ ;
		if ( scalar( @cols ) != 5 ) 
		{
			Fail( "The line in sample sheet file has wrong format: ".$_."!\n" ) ;
		}

		++$singleCnt if ( $cols[0] == 1 ) ;
		++$mateCnt if ( $cols[0] == 2 ) ;

		push @sampleSheet, \@cols ;
	}
	
	# push the files to centrifuge arguments
	my $i ;
	my $ssCnt = scalar( @sampleSheet ) ;
	for ( $i = 0 ; $i < $ssCnt ; ++$i )
	{
		my @cols = @{ $sampleSheet[$i] } ;
		if ( $cols[0] == 1 )
		{
			push @bt2w_args, ( "-U", $cols[1] ) ;
		}
		elsif ( $cols[0] == 2 )
		{
			push @bt2w_args, ( "-1", $cols[1], "-2", $cols[2] ) ;
		}
		
	}
	
	my @fileType = ( 2, 1 ) ;
	my $idx = 0 ;
	for my $f (@fileType )
	{
		for ( $i = 0 ; $i < scalar( $ssCnt ) ; ++$i )
		{
			if ( @{ $sampleSheet[ $i ] }[0] == $f )
			{
				$sampleSheetOrder[ $idx ] = $i ;
				++$idx ;
			}
		}
	}

	close FP1 ;
}

# Determine whether we need to add two extra columns for seq and qual to out-fmt
if ( $needReadSeq == 1 ) #&& ( $tabFmtOptIdx == 0 || $outputFmtSam == 1 ) )
{
	my $i ;
	my $needAdd = 1 ;
	if ( $tabFmtOptIdx != 0 )
	{
		my @cols = split /,/, $bt2_args[ $tabFmtOptIdx ] ;
		foreach my $f (@cols)
		{
			if ( $f eq "readSeq" )
			{
				$needAdd = 0 ;		
				last ;
			}
		}

	}
	else
	{
		push @bt2_args, "--tab-fmt-cols" ;
		push @bt2_args, "readID,seqID,taxID,score,2ndBestScore,hitLength,queryLength,numMatches" ;
		$tabFmtOptIdx = scalar( @bt2_args ) - 1 ;
	}
	
	if ( $needAdd )
	{
		$removeSeqCols = 1 ;
		$bt2_args[ $tabFmtOptIdx ] .= ",readSeq,readQual" ; 
	}
}

# If the user asked us to redirect some reads to files, or to suppress
# unaligned reads, then we need to capture the output from Centrifuge and pass it
# through this wrapper.
my $passthru = 0;
if(scalar(keys %read_fns) > 0 || $no_unal || defined $sampleSheetFile ) {
	$passthru = 1;
	push @bt2_args, "--passthrough";
	$cap_out = "-";
	for(my $i = 0; $i < scalar(@bt2_args); $i++) {
		next unless defined($bt2_args[$i]);
		my $arg = $bt2_args[$i];
		if($arg eq "-S" || $arg eq "--output") {
			$i < scalar(@bt2_args)-1 || Fail("-S/--output takes an argument.\n");
			$cap_out = $bt2_args[$i+1];
			$bt2_args[$i] = undef;
			$bt2_args[$i+1] = undef;
		}
	}
}
my @tmp = ();
for (@bt2_args) { push(@tmp, $_) if defined($_); }
@bt2_args = @tmp;

my @unps = ();
my @mate1s = ();
my @mate2s = ();
my @to_delete = ();
my $temp_dir = "/tmp";
my $bam_out = 0;
my $ref_str = undef;
my $no_pipes = 0;
my $keep = 0;
my $verbose = 0;
my $readpipe = undef;
my $log_fName = undef;
my $help = 0;
my $createNewPipe = 0  ;

my @bt2w_args_cp = (@bt2w_args>0) ? @bt2w_args : @bt2_args;
Getopt::Long::Configure("pass_through","no_ignore_case");

my @old_ARGV = @ARGV;
@ARGV = @bt2w_args_cp;

GetOptions(
	"1=s"                           => \@mate1s,
	"2=s"                           => \@mate2s,
	"reads|U=s"                     => \@unps,
	"temp-directory=s"              => \$temp_dir,
	"bam"                           => \$bam_out,
	"no-named-pipes"                => \$no_pipes,
	"ref-string|reference-string=s" => \$ref_str,
	"keep"                          => \$keep,
	"verbose"                       => \$verbose,
	"log-file=s"                    => \$log_fName,
	"help|h"                        => \$help
);

@ARGV = @old_ARGV;

my $old_stderr;

if ($log_fName) {
    open($old_stderr, ">&STDERR") or Fail("Cannot dup STDERR!\n");
    open(STDERR, ">", $log_fName) or Fail("Cannot redirect to log file $log_fName.\n");
}

Info("Before arg handling:\n");
Info("  Wrapper args:\n[ @bt2w_args ]\n");
Info("  Binary args:\n[ @bt2_args ]\n");

sub cat_file($$) {
	my ($ifn, $ofh) = @_;
	my $ifh = undef;
	if($ifn =~ /\.gz$/) {
		open($ifh, "gzip -dc $ifn |") ||
			 Fail("Could not open gzipped read file: $ifn \n");
	} elsif($ifn =~ /\.bz2/) {
		open($ifh, "bzip2 -dc $ifn |") ||
			Fail("Could not open bzip2ed read file: $ifn \n");
	} else {
		open($ifh, $ifn) || Fail("Could not open read file: $ifn \n");
	}
	while(readline $ifh) { print {$ofh} $_; }
	close($ifh);
}

# Return non-zero if and only if the input should be wrapped (i.e. because
# it's compressed).
sub wrapInput($$$) {
	my ($unps, $mate1s, $mate2s) = @_;
	for my $fn (@$unps, @$mate1s, @$mate2s) {
		return 1 if $fn =~ /\.gz$/ || $fn =~ /\.bz2$/;
	}
	return 0;
}

sub Info {
    if ($verbose) {
        print STDERR "(INFO): " ,@_;
    }
}

sub Error {
    my @msg = @_;
    $msg[0] = "(ERR): ".$msg[0];
    printf STDERR @msg;
}

sub Fail {
    Error(@_);
    die("Exiting now ...\n");    
}

sub Extract_IndexName_From {
    my $index_opt = $ref_str ? '--index' : '-x';
    for (my $i=0; $i<@_; $i++) {
        if ($_[$i] eq $index_opt){
            return $_[$i+1];
        }
    }
    Info("Cannot find any index option (--reference-string, --ref-string or -x) in the given command line.\n");    
}

if(wrapInput(\@unps, \@mate1s, \@mate2s)) {
	if ( defined $sampleSheetFile )
	{
		$createNewPipe = 1 ;
		if(scalar(@mate2s) > 0) {
			#
			# Wrap paired-end inputs
			#
			# Put reads into temporary files or fork off processes to feed named pipes
			scalar(@mate2s) == scalar(@mate1s) ||
				Fail("Different number of files specified with --reads/-1 as with -2\n");
			for ( my $i = 0 ; $i < scalar( @mate2s ) ; ++$i )
			{
				# Make a named pipe for delivering mate #1s
				my $m1fn = "$temp_dir/$$"."_$i"."inpipe1";
				push @to_delete, $m1fn;
				push @bt2_args, "-1 $m1fn";
				if(!$no_pipes) {
					mkfifo($m1fn, 0700) || Fail("mkfifo($m1fn) failed.\n");
				}
				
				# Make a named pipe for delivering mate #2s
				my $m2fn = "$temp_dir/$$."."_$i"."inpipe2";
				push @to_delete, $m2fn;
				push @bt2_args, "-2 $m2fn";
				if(!$no_pipes) {
					mkfifo($m2fn, 0700) || Fail("mkfifo($m2fn) failed.\n");
				}
			}
		}
		if(scalar(@unps) > 0) {
			#
			# Wrap unpaired inputs.
			#

			for ( my $i = 0 ; $i < scalar( @unps ) ; ++$i )
			{
				# Make a named pipe for delivering unpaired reads
				my $ufn = "$temp_dir/$$"."_$i".".unp";
				push @to_delete, $ufn;
				push @bt2_args, "-U $ufn";
				if(!$no_pipes) {
					mkfifo($ufn, 0700) || Fail("mkfifo($ufn) failed.\n");
				}
			}
		}
	}
	else
	{
		if(scalar(@mate2s) > 0) {
			#
			# Wrap paired-end inputs
			#
			# Put reads into temporary files or fork off processes to feed named pipes
			scalar(@mate2s) == scalar(@mate1s) ||
				Fail("Different number of files specified with --reads/-1 as with -2\n");
			# Make a named pipe for delivering mate #1s
			my $m1fn = "$temp_dir/$$.inpipe1";
			push @to_delete, $m1fn;
			push @bt2_args, "-1 $m1fn";
			# Create named pipe 1 for writing
			if(!$no_pipes) {
				mkfifo($m1fn, 0700) || Fail("mkfifo($m1fn) failed.\n");
			}
			my $pid = 0;
			$pid = fork() unless $no_pipes;
			if($pid == 0) {
				# Open named pipe 1 for writing
				open(my $ofh, ">$m1fn") || Fail("Can't open '$m1fn' for writing\n");
				for my $ifn (@mate1s) { cat_file($ifn, $ofh); }
				close($ofh);
				exit 0 unless $no_pipes;
			}
			# Make a named pipe for delivering mate #2s
			my $m2fn = "$temp_dir/$$.inpipe2";
			push @to_delete, $m2fn;
			push @bt2_args, "-2 $m2fn";
			# Create named pipe 2 for writing
			if(!$no_pipes) {
				mkfifo($m2fn, 0700) || Fail("mkfifo($m2fn) failed.\n");
			}
			$pid = 0;
			$pid = fork() unless $no_pipes;
			if($pid == 0) {
				# Open named pipe 2 for writing
				open(my $ofh, ">$m2fn") || Fail("Can't open '$m2fn' for writing.\n");
				for my $ifn (@mate2s) { cat_file($ifn, $ofh); }
				close($ofh);
				exit 0 unless $no_pipes;
			}
		}
		if(scalar(@unps) > 0) {
			#
			# Wrap unpaired inputs.
			#
			# Make a named pipe for delivering unpaired reads
			my $ufn = "$temp_dir/$$.unp";
			push @to_delete, $ufn;
			push @bt2_args, "-U $ufn";
			# Create named pipe 2 for writing
			if(!$no_pipes) {
				mkfifo($ufn, 0700) || Fail("mkfifo($ufn) failed.\n");
			}
			my $pid = 0;
			$pid = fork() unless $no_pipes;
			if($pid == 0) {
				# Open named pipe 2 for writing
				open(my $ofh, ">$ufn") || Fail("Can't open '$ufn' for writing.\n");
				for my $ifn (@unps) { cat_file($ifn, $ofh); }
				close($ofh);
				exit 0 unless $no_pipes;
			}
		}
	}
} else {
	if(scalar(@mate2s) > 0) {
		# Just pass all the mate arguments along to the binary
		push @bt2_args, ("-1", join(",", @mate1s));
		push @bt2_args, ("-2", join(",", @mate2s));
	}
	if(scalar(@unps) > 0) {
		push @bt2_args, ("-U", join(",", @unps));
	}
}

if(defined($ref_str)) {
	my $ofn = "$temp_dir/$$.ref_str.fa";
	open(my $ofh, ">$ofn") ||
		Fail("could not open temporary fasta file '$ofn' for writing.\n");
	print {$ofh} ">1\n$ref_str\n";
	close($ofh);
	push @to_delete, $ofn;
	system("$build_bin $ofn $ofn") == 0 ||
		Fail("centrifuge-build returned non-0 exit level.\n");
	push @bt2_args, ("--index", "$ofn");
	push @to_delete, ("$ofn.1.".$idx_ext, "$ofn.2.".$idx_ext, 
	                  "$ofn.3.".$idx_ext, "$ofn.4.".$idx_ext,
			  "$ofn.5.".$idx_ext, "$ofn.6.".$idx_ext,
	                  "$ofn.rev.1.".$idx_ext, "$ofn.rev.2.".$idx_ext,
			  "$ofn.rev.5.".$idx_ext, "$ofn.rev.6.".$idx_ext);
}

Info("After arg handling:\n");
Info("  Binary args:\n[ @bt2_args ]\n");

my $index_name = Extract_IndexName_From(@bt2_args);

my $debug_str = ($debug ? "-debug" : "");

# Construct command invoking centrifuge-class
my $cmd = "$align_prog$debug_str --wrapper basic-0 ".join(" ", @bt2_args);

# Possibly add read input on an anonymous pipe
$cmd = "$readpipe $cmd" if defined($readpipe);

# The function removes the two extra columns that we added to get the read seq and qual
sub RemoveSeqCols
{
	my $line = $_[0] ;
	my @cols = split /\t/, $line ;
	pop @cols ;
	pop @cols ;
	my $tab = "\t" ;
	return join( $tab, @cols ) ;
}

Info("$cmd\n");
my $ret;

sub GetSampleSheetOutputFileName
{
	my $sampleIdx = $_[0] ;
	return @{ $sampleSheet[ $sampleSheetOrder[ $sampleIdx ] ] }[3] ;

}

sub GetSampleSheetReportFileName
{
	my $sampleIdx = $_[0] ;
	return @{ $sampleSheet[ $sampleSheetOrder[ $sampleIdx ] ] }[4] ;
}

sub WritePipe
{
	my $i = $_[0] ;
	if ( $i < scalar( @mate2s ) )
	{
		my $m1fn = "$temp_dir/$$"."_$i"."inpipe1";

		# Create named pipe 1 for writing
		#if(!$no_pipes) {
		#	mkfifo($m1fn, 0700) || Fail("mkfifo($m1fn) failed.\n");
		#}
		my $pid = 0;
		$pid = fork() unless $no_pipes;
		if($pid == 0) {
		# Open named pipe 1 for writing
			open(my $ofh, ">$m1fn") || Fail("Can't open '$m1fn' for writing\n");
			cat_file($mate1s[$i], $ofh); 
			close($ofh);
			exit 0 unless $no_pipes;
		}

		my $m2fn = "$temp_dir/$$."."_$i"."inpipe2";

		#if(!$no_pipes) {
		#	mkfifo($m2fn, 0700) || Fail("mkfifo($m2fn) failed.\n");
		#}
		$pid = 0;
		$pid = fork() unless $no_pipes;
		if($pid == 0) {
			# Open named pipe 2 for writing
			open(my $ofh, ">$m2fn") || Fail("Can't open '$m2fn' for writing.\n");
			cat_file( $mate2s[$i], $ofh); 
			close($ofh);
			exit 0 unless $no_pipes;
		}
	}
	elsif ( $i < scalar( @mate2s ) + scalar( @unps ) )
	{
		$i -= scalar( @mate2s ) ;
		my $ufn = "$temp_dir/$$"."_$i".".unp";
		#if(!$no_pipes) {
		#	mkfifo($ufn, 0700) || Fail("mkfifo($ufn) failed.\n");
		#}
		my $pid = 0;
		$pid = fork() unless $no_pipes;
		if($pid == 0) {
			# Open named pipe 2 for writing
			open(my $ofh, ">$ufn") || Fail("Can't open '$ufn' for writing.\n");
			cat_file($unps[$i], $ofh); 
			close($ofh);
			exit 0 unless $no_pipes;
		}

	}
}

WritePipe( 0 ) if ( $createNewPipe ) ;
if(defined($cap_out)) {
	# Open Centrifuge pipe
	open(BT, "$cmd |") || Fail("Could not open Centrifuge pipe: '$cmd |'\n");
	# Open output pipe
	my $ofh = *STDOUT;
	
	my $sampleIdx = 0 ;
	if ( defined $sampleSheetFile )
	{
		my $file = GetSampleSheetOutputFileName( $sampleIdx ) ;
		open ( $ofh, ">$file" ) || Fail( "Could not open output file '$file' for writing.\n" ) ;
	}
	else
	{
		if($cap_out ne "-") {
			open($ofh, ">$cap_out") ||
				Fail("Could not open output file '$cap_out' for writing.\n");
		}
	}

	my @fhs_to_close = ();
	my %read_fhs = ();
	for my $i ("al", "un", "al-conc", "un-conc") {
		if(defined($read_fns{$i})) {
			my ($vol, $base_spec_dir, $base_fname) = File::Spec->splitpath($read_fns{$i});
			if (-d $read_fns{$i}) {
				$base_spec_dir = $read_fns{$i};
				$base_fname = undef;
			}
			if($i =~ /-conc$/) {
# Open 2 output files, one for mate 1, one for mate 2
				my ($fn1, $fn2);
				if ($base_fname) {
					($fn1, $fn2) = ($base_fname,$base_fname);
				}
				else {
					($fn1, $fn2) = ($i.'-mate',$i.'-mate');
				}
				if($fn1 =~ /%/) {
					$fn1 =~ s/%/1/g; $fn2 =~ s/%/2/g;
				} elsif($fn1 =~ /\.[^.]*$/) {
					$fn1 =~ s/\.([^.]*)$/.1.$1/;
					$fn2 =~ s/\.([^.]*)$/.2.$1/;
				} else {
					$fn1 .= ".1";
					$fn2 .= ".2";
				}
				$fn1 = File::Spec->catpath($vol,$base_spec_dir,$fn1);
				$fn2 = File::Spec->catpath($vol,$base_spec_dir,$fn2);
				$fn1 ne $fn2 || Fail("$fn1\n$fn2\n");
				my ($redir1, $redir2) = (">$fn1", ">$fn2");
				$redir1 = "| gzip -c $redir1"  if $read_compress{$i} eq "gzip";
				$redir1 = "| bzip2 -c $redir1" if $read_compress{$i} eq "bzip2";
				$redir2 = "| gzip -c $redir2"  if $read_compress{$i} eq "gzip";
				$redir2 = "| bzip2 -c $redir2" if $read_compress{$i} eq "bzip2";
				open($read_fhs{$i}{1}, $redir1) || Fail("Could not open --$i mate-1 output file '$fn1'\n");
				open($read_fhs{$i}{2}, $redir2) || Fail("Could not open --$i mate-2 output file '$fn2'\n");
				push @fhs_to_close, $read_fhs{$i}{1};
				push @fhs_to_close, $read_fhs{$i}{2};
			} else {
				my $redir = ">".File::Spec->catpath($vol,$base_spec_dir,$i."-seqs");
				if ($base_fname) {
					$redir = ">$read_fns{$i}";
				}
				$redir = "| gzip -c $redir"  if $read_compress{$i} eq "gzip";
				$redir = "| bzip2 -c $redir" if $read_compress{$i} eq "bzip2";
				open($read_fhs{$i}, $redir) || Fail("Could not open --$i output file '$read_fns{$i}'\n");
				push @fhs_to_close, $read_fhs{$i};
			}
		}
	}

	my $seqIndex = -1 ;
	my $qualIndex = -1 ;
	my $readIdIndex = -1 ;
	my $outputHeader = "" ;

	if ( scalar(keys %read_fhs) != 0 )
	{
		if ( $outputFmtSam == 0 )
		{
			while ( 1 )
			{
				$outputHeader = <BT> ;
				last if ( $outputHeader =~ /readID/ || $outputFmtSam ) ;
			}
			my @cols = split /\t/, $outputHeader ;
			for ( my $i = 0 ; $i < scalar( @cols ) ; ++$i )
			{
				if ( $cols[$i] =~ /readSeq/ )
				{
					$seqIndex = $i ;
				}
				elsif ( $cols[$i] =~ /readQual/ )
				{
					$qualIndex = $i ;
				}
				elsif ( $cols[$i] =~ /readID/ )
				{
					$readIdIndex = $i ;
				}
			}
			if ( $seqIndex == -1 && scalar( keys %read_fhs) == 0 )
			{
				Error( "Must use readSeq in --tabFmtCols in order to output unaligned reads." )  ;
			}

			$outputHeader = RemoveSeqCols( $outputHeader )."\n" if ( $removeSeqCols == 1 ) ;
			print {$ofh} $outputHeader ;
		}
		else
		{
			$seqIndex = 9 ;
			$qualIndex = 10 ;
			$readIdIndex = 0 ;
		}
	}
	else
	{
		$outputHeader = <BT> ;
		print {$ofh} $outputHeader ;
	}

	while(<BT>) {
		chomp;
		my $filt = 0;

		if ( defined $sampleSheetFile )
		{	
			if ( $_ eq "#File_End_Here" )
			{
				close( $ofh ) ;
				rename( "centrifuge_report_$sampleIdx.tsv", GetSampleSheetReportFileName( $sampleIdx ) ) ;
				
				++$sampleIdx ;
				if ( $sampleIdx < scalar( @sampleSheet ) )
				{
					my $file = GetSampleSheetOutputFileName( $sampleIdx ) ;
					open ( $ofh, ">$file" ) || Fail( "Could not open output file '$file' for writing.\n" ) ;
					print {$ofh} $outputHeader ;
					
					WritePipe( $sampleIdx) if ( $createNewPipe ) ;
				}
				next ;
			}
		}

		# originally this was @ sign for sam file, but we use # sign for comment in tsv here.
		unless(substr($_, 0, 1) eq "#" ) {
			# If we are supposed to output certain reads to files...
			#my $tab1_i = index($_, "\t") + 1;
			#my $tab2_i = index($_, "\t", $tab1_i);
			#my $fl = substr($_, $tab1_i, $tab2_i - $tab1_i);
			my $unal = 0 ;
			if ( /unclassified/ )
			{
				$unal = 1 ;
			}
			$filt = 1 if $no_unal && $unal;
			if($passthru) {
				if(scalar(keys %read_fhs) == 0 || $seqIndex == -1 ) {
					# Next line is read with some whitespace escaped
					# my $l = <BT>;
				} else {
					my @cols = split /\t/ ;
					my $isPaired = 0 ;
					my $pair = 0 ;
					if (  $cols[$seqIndex] =~ /_/ )
					{
						$pair = 1 ;
					}
					my $unp = !$pair ;

					# Next line is read with some whitespace escaped
					#my $l = <BT>;
					#chomp($l);
					#$l =~ s/%(..)/chr(hex($1))/eg;

					if((defined($read_fhs{un}) || defined($read_fhs{al})) && $unp) {
						my $l ;
						if ( $qualIndex != -1 )
						{
							$l = "@".$cols[ $readIdIndex ]."\n".$cols[$seqIndex]."\n+\n".$cols[$qualIndex]."\n" ;
						}
						else 
						{
							$l = ">".$cols[ $readIdIndex ]."\n".$cols[$seqIndex]."\n" ;
						}
						if($unal) {
							# Failed to align
							print {$read_fhs{un}} $l if defined($read_fhs{un});
						} else {
							# Aligned
							print {$read_fhs{al}} $l if defined($read_fhs{al});
						}
					}
					my $warnedAboutLength = 0 ;
					if((defined($read_fhs{"un-conc"}) || defined($read_fhs{"al-conc"})) && $pair) {
						my @seq = split /_/, $cols[$seqIndex] ;
						my @qual = ( substr( $cols[$qualIndex], 0, length( $seq[0] ) ), substr( $cols[$qualIndex], length( $seq[0] ) + 1 ) ) ;
						
						my $l1 ;
						my $l2 ;
						if ( $qualIndex != -1 )
						{
							$l1 = "@".$cols[ $readIdIndex ]."\n".$seq[0]."\n+\n".$qual[0]."\n" ;
						}
						else 
						{
							$l1 = ">".$cols[ $readIdIndex ]."\n".$seq[0]."\n" ;
						}
						if ( $qualIndex != -1 )
						{
							$l2 = "@".$cols[ $readIdIndex ]."\n".$seq[1]."\n+\n".$qual[1]."\n" ;
						}
						else 
						{
							$l2 = ">".$cols[ $readIdIndex ]."\n".$seq[1]."\n" ;
						}

						if     ( !$unal) {
							print {$read_fhs{"al-conc"}{1}} $l1 if defined($read_fhs{"al-conc"});
							print {$read_fhs{"al-conc"}{2}} $l2 if defined($read_fhs{"al-conc"});
						} else {
							print {$read_fhs{"un-conc"}{1}} $l1 if defined($read_fhs{"un-conc"});
							print {$read_fhs{"un-conc"}{2}} $l2 if defined($read_fhs{"un-conc"});
						}
					}
				}
			}
		}
		$_ = RemoveSeqCols( $_ ) if ( $removeSeqCols == 1 ) ;
		print {$ofh} "$_\n" if !$filt;
	}
	for my $k (@fhs_to_close) { close($k); }
	close($ofh);
	close(BT);
	$ret = $?;
} else {
	$ret = system($cmd);
}
if(!$keep) { for(@to_delete) { unlink($_); } }

if ($ret == -1) {
    Error("Failed to execute centrifuge-class: $!\n");
	exit 1;
} elsif ($ret & 127) {
	my $signm = "(unknown)";
	$signm = $signame[$ret & 127] if defined($signame[$ret & 127]);
	my $ad = "";
	$ad = "(core dumped)" if (($ret & 128) != 0);
    Error("centrifuge-class died with signal %d (%s) $ad\n", ($ret & 127), $signm);
	exit 1;
} elsif($ret != 0) {
	Error("centrifuge-class exited with value %d\n", ($ret >> 8));
}
exit ($ret >> 8);