hisat-3n/hisat2

#!/usr/bin/env perl

#
# Copyright 2015, Daehwan Kim <infphilo@gmail.com>
#
# This file is part of HISAT 2.
#
# HISAT 2 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.
#
# HISAT 2 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 HISAT 2.  If not, see <http://www.gnu.org/licenses/>.
#

# hisat2:
#
# A wrapper script for hisat2.  Provides various advantages over running
# hisat 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 ? 'hisat2-align-s' : 'hisat2-align-s.exe'; 
my $build_bin   = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe';               
my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe'; 
my $align_prog_s= File::Spec->catpath($vol,$script_path,$align_bin_s);
my $align_prog_l= File::Spec->catpath($vol,$script_path,$align_bin_l);
my $align_prog  = $align_prog_s;
my $read_stat_prog = File::Spec->catpath($vol,$script_path,"hisat2_read_statistics.py");
my $idx_ext_l     = 'ht2l';
my $idx_ext_s     = 'ht2'; 
my $idx_ext       = $idx_ext_s; 
my $seq_in_args = 0;
my $skip_read_stat = 0;
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 "$align_prog") ||
	Fail("Expected hisat2 to be in same directory with hisat2-align-s and hisat2-align-l:\n$script_path\n");

(-x "$read_stat_prog") || ($skip_read_stat = 1);

# Get description of arguments from HISAT so that we can distinguish HISAT
# args from wrapper args
sub getHt2Desc($) {
	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);
getHt2Desc(\%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 HISAT)
sub isWrapped($) { return defined($wrapped{$_[0]}); }

my @orig_argv = @ARGV;

my @ht2w_args = (); # options for wrapper
my @ht2_args  = (); # options for HISAT
my $saw_dd = 0;
for(0..$#ARGV) {
	if($ARGV[$_] eq "--") {
		$saw_dd = 1;
		next;
	}
	push @ht2w_args, $ARGV[$_] if !$saw_dd;
	push @ht2_args,  $ARGV[$_] if  $saw_dd;
}
if(!$saw_dd) {
	@ht2_args = @ht2w_args;
	@ht2w_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;
# Remove whitespace
for my $i (0..$#ht2_args) {
	$ht2_args[$i]=~ s/^\s+//; $ht2_args[$i] =~ s/\s+$//;
}

# We've handled arguments that the user has explicitly directed either to the
# wrapper or to hisat, now we capture some of the hisat arguments that
# ought to be handled in the wrapper
for(my $i = 0; $i < scalar(@ht2_args); $i++) {
	next unless defined($ht2_args[$i]);
	my $arg = $ht2_args[$i];
	my @args = split(/=/, $arg);
	if(scalar(@args) > 2) {
		$args[1] = join("=", @args[1..$#args]);
	}
	$arg = $args[0];
	if($arg eq "-U" || $arg eq "--unpaired") {
		$ht2_args[$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 @ht2w_args, ("-U", $a); }
		} else {
			# Argument is in the next token
			$i < scalar(@ht2_args)-1 || Fail("Argument expected in next token!\n");
			$i++;
			my @args = split(/,/, $ht2_args[$i]);
			for my $a (@args) { push @ht2w_args, ("-U", $a); }
			$ht2_args[$i] = undef;
		}
	}
	if($arg =~ /^--?([12])/ && $arg !~ /^--?12/) {
		my $mate = $1;
		$ht2_args[$i] = undef;
		$arg =~ s/^--?[12]//;
		if($arg ne "") {
			# Argument was part of this token
			my @args = split(/,/, $arg);
			for my $a (@args) { push @ht2w_args, ("-$mate", $a); }
		} else {
			# Argument is in the next token
			$i < scalar(@ht2_args)-1 || Fail("Argument expected in next token!\n");
			$i++;
			my @args = split(/,/, $ht2_args[$i]);
			for my $a (@args) { push @ht2w_args, ("-$mate", $a); }
			$ht2_args[$i] = undef;
		}
	}
	if($arg eq "--debug") {
		$debug = 1;
		$ht2_args[$i] = undef;
	}
	if($arg eq "--no-unal") {
		$no_unal = 1;
		$ht2_args[$i] = undef;
	}
	if($arg eq "--large-index") {
		$large_idx = 1;
		$ht2_args[$i] = undef;
	}
	if($arg eq "--skip-read-lengths") {
		$skip_read_stat = 1;
		$ht2_args[$i] = undef
	}
	if($arg eq "-c") {
		$seq_in_args = 1;
	}
	for my $rarg ("un-conc", "al-conc", "al-conc-disc", "un", "al") {
		if($arg =~ /^--${rarg}$/ || $arg =~ /^--${rarg}-gz$/ || $arg =~ /^--${rarg}-bz2$/) {
			$ht2_args[$i] = undef;
			if(scalar(@args) > 1 && $args[1] ne "") {
				$read_fns{$rarg} = $args[1];
			} else {
				$i < scalar(@ht2_args)-1 || Fail("--${rarg}* option takes an argument.\n");
				$read_fns{$rarg} = $ht2_args[$i+1];
				$ht2_args[$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 the user asked us to redirect some reads to files, or to suppress
# unaligned reads, then we need to capture the output from HISAT and pass it
# through this wrapper.
my $passthru = 0;
if(scalar(keys %read_fns) > 0 || $no_unal) {
	$passthru = 1;
	push @ht2_args, "--passthrough";
	$cap_out = "-";
	for(my $i = 0; $i < scalar(@ht2_args); $i++) {
		next unless defined($ht2_args[$i]);
		my $arg = $ht2_args[$i];
		if($arg eq "-S" || $arg eq "--output") {
			$i < scalar(@ht2_args)-1 || Fail("-S/--output takes an argument.\n");
			$cap_out = $ht2_args[$i+1];
			$ht2_args[$i] = undef;
			$ht2_args[$i+1] = undef;
		}
	}
}
my @tmp = ();
for (@ht2_args) { push(@tmp, $_) if defined($_); }
@ht2_args = @tmp;

my @unps = ();
my @mate1s = ();
my @mate2s = ();
my @to_delete = ();
my @to_kills = ();
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 @ht2w_args_cp = (@ht2w_args>0) ? @ht2w_args : @ht2_args;
Getopt::Long::Configure("pass_through","no_ignore_case");

my @old_ARGV = @ARGV;
@ARGV = @ht2w_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[ @ht2w_args ]\n");
Info("  Binary args:\n[ @ht2_args ]\n");

# check read lengths
# if read_files have more than 1 files, use first one,
my @read_files = (scalar(@unps) > 0) ? @unps : @mate1s;
if ((scalar(@read_files) > 0)
		&& ($seq_in_args == 0)
		&& ($skip_read_stat == 0)) {
	Info("Check read length: $read_files[0]\n");
	my $cmd = "'$read_stat_prog' $read_files[0]";
	my $read_len_str = "";

	open(my $fh, "$cmd |") || Fail("Failed to run command '$cmd'\n");
	while(readline $fh) {
		chomp;
		next if /^\s*$/;
		my @ts = split(/ /);
		if (scalar(@ts) > 4) {
			$read_len_str = $ts[4];
		} else {
			$read_len_str = "";
		}
	}
	close($fh);

	if (($read_len_str ne "") && ($read_len_str ne "0")) {
		Info("Read Length String: $read_len_str\n");
		push @ht2_args, ("--read-lengths", $read_len_str);
	}
}

sub check_file_exist($$$) {
	my ($unps, $mate1s, $mate2s) = @_;
	for my $fn (@$unps, @$mate1s, @$mate2s) {
		if (not -f $fn) {
			Fail("Read file '%s' doesn't exist\n", $fn);
			return 1;
		}
	}
	return 0;
}

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){
			my $idx_basename = $_[$i+1];
			my @idx_filenames = glob($idx_basename . "*.ht2{,l}");
			unless(@idx_filenames) {
				if(exists $ENV{"HISAT2_INDEXES"}) {
					@idx_filenames = glob("$ENV{'HISAT2_INDEXES'}/$idx_basename" . "ht2{,l}");
				}

				if(!@idx_filenames) {
					Fail("\"" . $idx_basename . "\" does not exist\n");
				}
				$idx_basename = "$ENV{'HISAT2_INDEXES'}/$idx_basename"
			}

            return $idx_basename;
        }
    }
    Info("Cannot find any index option (--reference-string, --ref-string or -x) in the given command line.\n");    
}

if($seq_in_args == 0) {
	check_file_exist(\@unps, \@mate1s, \@mate2s);
}

if(wrapInput(\@unps, \@mate1s, \@mate2s)) {
	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/$$.inpipe1";
		push @to_delete, $m1fn;
		push @ht2_args, "-1 $m1fn";
		# Create named pipe 1 for writing
		if(!$no_pipes) {
			mkfifo($m1fn, 0700) || Fail("mkfifo($m1fn) failed.\n");
		}
		my $pid = 0;
		$pid = fork() unless $no_pipes;
		push @to_kills, $pid unless $no_pipes;
		if($pid == 0) {
			# Open named pipe 1 for writing
			open(my $ofh, ">$m1fn") || Fail("Can't open '$m1fn' for writing\n");
			for my $ifn (@mate1s) { cat_file($ifn, $ofh); }
			close($ofh);
			exit 0 unless $no_pipes;
		}
		# Make a named pipe for delivering mate #2s
		my $m2fn = "$temp_dir/$$.inpipe2";
		push @to_delete, $m2fn;
		push @ht2_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;
		push @to_kills, $pid 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 @ht2_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 @ht2_args, ("-1", join(",", @mate1s));
		push @ht2_args, ("-2", join(",", @mate2s));
	}
	if(scalar(@unps) > 0) {
		push @ht2_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 $ofn") == 0 ||
		Fail("hisat2-build returned non-0 exit level.\n");
	push @ht2_args, ("--index", "$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,
			  "$ofn.7.".$idx_ext, "$ofn.8.".$idx_ext);
}

Info("After arg handling:\n");
Info("  Binary args:\n[ @ht2_args ]\n");

my $index_name = Extract_IndexName_From(@ht2_args);

if ($large_idx) {
    Info("Using a large index enforced by user.\n");
    $align_prog  = $align_prog_l;
    $idx_ext     = $idx_ext_l;
    if (not -f $index_name.".1.".$idx_ext_l) {
        Fail("Cannot find the large index ${index_name}.1.${idx_ext_l}\n");
    }
    Info("Using large index (${index_name}.1.${idx_ext_l}).\n");
}
else {
    if ((-f $index_name.".1.".$idx_ext_l) && 
        (not -f $index_name.".1.".$idx_ext_s)) {
        Info("Cannot find a small index but a large one seems to be present.\n");
        Info("Switching to using the large index (${index_name}.1.${idx_ext_l}).\n");
        $align_prog  = $align_prog_l;
        $idx_ext     = $idx_ext_l;
    }
    else {
        Info("Using the small index (${index_name}.1.${idx_ext_s}).\n")
    }
}

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

# Construct command invoking hisat2-align
my $cmd = "'$align_prog$debug_str' --wrapper basic-0 ".join(" ", @ht2_args);

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

Info("$cmd\n");
my $ret;
if(defined($cap_out)) {
	# Open HISAT2 pipe
	open(HT, "$cmd |") || Fail("Could not open HISAT2 pipe: '$cmd |'\n");
	# Open output pipe
	my $ofh = *STDOUT;
	my @fhs_to_close = ();
	if($cap_out ne "-") {
		open($ofh, ">$cap_out") ||
			Fail("Could not open output file '$cap_out' for writing.\n");
	}
	my %read_fhs = ();
	for my $i ("al", "un", "al-conc", "al-conc-disc", "un-conc") {
		if(defined($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$/ || $i =~ /-conc-disc$/) {
				# 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};
			}
		}
	}
	while(<HT>) {
		chomp;
		my $filt = 0;
		unless(substr($_, 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 $unal = ($fl & 4) != 0;
			my $secondary = ($fl & 256) != 0;
			$filt = 1 if $no_unal && $unal;
			if($passthru) {
				if(scalar(keys %read_fhs) == 0) {
					# Next line is read with some whitespace escaped
					my $l = <HT>;
				} else {
					my $mate1 = (($fl &  64) != 0);
					my $mate2 = (($fl & 128) != 0);
					my $unp = !$mate1 && !$mate2;
					my $pair = !$unp;
					# Next line is read with some whitespace escaped
					my $l = <HT>;
					chomp($l);
					$l =~ s/%(..)/chr(hex($1))/eg;
					if((defined($read_fhs{un}) || defined($read_fhs{al})) && $unp && !$secondary) {
						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});
						}
					}
					if((defined($read_fhs{"un-conc"}) || defined($read_fhs{"al-conc"}) || defined($read_fhs{"al-conc-disc"})) && $pair && !$secondary) {
						my $conc = (($fl &   2) != 0);
						my $conc_disc = ($fl & 4) == 0 || ($fl & 8) == 0;
						if($conc && $mate1) {
							print {$read_fhs{"al-conc"}{1}} $l if defined($read_fhs{"al-conc"});
						} elsif($conc && $mate2) {
							print {$read_fhs{"al-conc"}{2}} $l if defined($read_fhs{"al-conc"});
						} elsif(!$conc && $mate1) {
							print {$read_fhs{"un-conc"}{1}} $l if defined($read_fhs{"un-conc"});
						} elsif(!$conc && $mate2) {
							print {$read_fhs{"un-conc"}{2}} $l if defined($read_fhs{"un-conc"});
						}
						if($conc_disc && $mate1) {
							print {$read_fhs{"al-conc-disc"}{1}} $l if defined($read_fhs{"al-conc-disc"});
						} elsif($conc_disc && $mate2) {
							print {$read_fhs{"al-conc-disc"}{2}} $l if defined($read_fhs{"al-conc-disc"});
						}
					}
				}
			}
		}
		print {$ofh} "$_\n" if !$filt;
	}
	for my $k (@fhs_to_close) { close($k); }
	close($ofh);
	close(HT);
	$ret = $?;
} else {
	$ret = system($cmd);
}
kill 'TERM', @to_kills;

if(!$keep) { for(@to_delete) { unlink($_); } }

if ($ret == -1) {
    Error("Failed to execute hisat2-align: $!\n");
	exit 1;
} elsif ($ret & 127) {
	my $signm = "(unknown)";
	$signm = $signame[$ret & 127] if defined($signame[$ret & 127]);
	my $ad = "";
	$ad = "(core dumped)" if (($ret & 128) != 0);
    Error("hisat2-align died with signal %d (%s) $ad\n", ($ret & 127), $signm);
	exit 1;
} elsif($ret != 0) {
	Error("hisat2-align exited with value %d\n", ($ret >> 8));
}
exit ($ret >> 8);