#! /usr/local/bin/perl

# dos2unix.pl by David Efflandt <efflandt@xnet.com>
# Modification of script from "Learning perl" p.353
# O'Reilly & Associates, Inc.
#
# Run after transfering text files from DOS to UNIX system.
# Strips carriage returns from DOS files for use UNIX.
# Transfers file permissions to new file (except suid bit).
#
#	Usage:\tdos2unix.pl FILELIST
#	where FILELIST = one or more filenames
#
# If you edit this file in DOS you can run it on itself by typing:
#	perl dos2unix.pl dos2unix.pl
#
# Modify variables below for other search and replace functions.

$find = "\r";	# find this
$sub = undef;	# substitute with this
$rm_bak = 1;	# remove old file after conversion: 0 = no, 1 = yes

while (<>) {
	if ($ARGV ne $oldargv) {
		($dev,$ino,$mode,$nlink,$uid,$gid) = stat($ARGV);
		$backup = $ARGV . '.bak';
		rename($ARGV, $backup);
		open (ARGVOUT, ">$ARGV");
		chmod $mode, $ARGV;
		select(ARGVOUT);
		$oldargv = $ARGV;
	}
	s/$find/$sub/;
} continue {
	print;
	if (eof) {
		print STDOUT "Converted: $oldargv\n";
		unlink $backup if $rm_bak;
	}
}
select(STDOUT);
#________________________________________________________________________
# Title     : read_dir_names_only
# Usage     : @all_dirs_list = @{&read_dir_names_only(\$absolute_path_dir_name, ....)};
# Function  : read any dir names and and then put in array.
# Example   :
# Warning   : This does not report '.', '..'
#             Only file names are reported. Compare with &read_any_dir
# Class     :
# Keywords  :
# Options   :
# Package   :
# Reference :
# Returns   : one ref. of array.
# Tips      :
# Argument  : takes one or more scaler references. ('.', \$path, $path, ... )
# Todo      :
# Author    : A Biomatic
# Version   : 3.1
# Used in   :
# Enclosed  :
#--------------------------------------------------------------------
sub read_dir_names_only{
  my($in_dir, $i,$k, @possible_dirs,
	  @final_files, $full_dir, $pwd, $path,@read_files);
  $pwd=`pwd`; chomp($pwd); $full_dir=1;
  for($k=0; $k < @_; $k++){
	 if   ( ($_[$k] eq '.') || !(defined($_[$k]))){  $in_dir=$pwd;  }
	 elsif(!(ref($_[$k]))){   $in_dir=$_[$k];   }
	 elsif(ref($_[$k])){      $in_dir =${$_[$k]};    }
	 if($in_dir =~ /^([\w\-\.]+)$/){  $in_dir="$pwd\/$in_dir"; $full_dir = 0; }
	 else{ $full_dir =1; }
	 ##########  Main READING PART ##########
	 opendir(DIR1,"$in_dir");
	 @read_files = readdir(DIR1);
	 for($i=0; $i < @read_files; $i ++){
		$read_files[$i]="$in_dir\/$read_files[$i]";
		if( ($read_files[$i] !~ /\/\.\.?$/) && ( -d $read_files[$i]) ){
		  $read_files[$i]=~s/\.\///; ## removing ./ in front of dirs (in bash)
		  push(@final_files, "$read_files[$i]");
		}
	 }
  }
  return([sort @final_files]);
}