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comparison getSomaticPindel.pl @ 0:acc8d8bfeb9a

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author jjohnson
date Wed, 08 Feb 2012 16:59:24 -0500
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1 #!/usr/bin/perl -w
2
3 use strict;
4 use Carp;
5 use Getopt::Long;
6 use English;
7 use Pod::Usage;
8 use Data::Dumper;
9
10 my ( $help, $man, $version, $usage );
11 my ($infile, $outfile);
12 my $optionOK = GetOptions(
13 'h|help|?' => \$help,
14 'man' => \$man,
15 'usage' => \$usage,
16 'v|version' => \$version,
17 'i|input=s' => \$infile,
18 'o|output=s' => \$outfile,
19 );
20
21 pod2usage(2) if($man);
22 pod2usage( -verbose => 99, -sections => "USAGE|REQUIRED ARGUMENTS|OPTIONS" )
23 if($help or $usage or !$infile or !$outfile);
24 pod2usage( -verbose => 99, -sections => "VERSION") if($version);
25
26 open my $IN "<$infile" or croak "can't open $infile:$OS_ERROR";
27 while(my $line = <$IN>) {
28
29 }
30 =head1 NAME
31
32 <application name> - <One-line description of application's purpose>
33
34
35 =head1 VERSION
36
37 The initial template usually just has:
38
39 This documentation refers to <application name> version 0.0.1.
40
41
42 =head1 USAGE
43
44 # Brief working invocation example(s) here showing the most common usage(s)
45
46 # This section will be as far as many users ever read,
47 # so make it as educational and exemplary as possible.
48 =head1 REQUIRED ARGUMENTS
49
50 A complete list of every argument that must appear on the command line.
51 when the application is invoked, explaining what each of them does, any
52 restrictions on where each one may appear (i.e., flags that must appear
53 before or after filenames), and how the various arguments and options
54 may interact (e.g., mutual exclusions, required combinations, etc.)
55
56 If all of the application's arguments are optional, this section
57 may be omitted entirely.
58
59 =head1 OPTIONS
60
61 A complete list of every available option with which the application
62 can be invoked, explaining what each does, and listing any restrictions,
63 or interactions.
64
65 If the application has no options, this section may be omitted entirely.
66
67
68 =head1 DESCRIPTION
69
70 A full description of the application and its features.
71 May include numerous subsections (i.e., =head2, =head3, etc.).
72
73
74 =head1 DIAGNOSTICS
75
76 A list of every error and warning message that the application can generate
77 (even the ones that will "never happen"), with a full explanation of each
78 problem, one or more likely causes, and any suggested remedies. If the
79 application generates exit status codes (e.g., under Unix), then list the exit
80 status associated with each error.
81
82 =head1 CONFIGURATION AND ENVIRONMENT
83
84 A full explanation of any configuration system(s) used by the application,
85 including the names and locations of any configuration files, and the
86 meaning of any environment variables or properties that can be set. These
87 descriptions must also include details of any configuration language used.
88
89
90 =head1 DEPENDENCIES
91
92 A list of all the other modules that this module relies upon, including any
93 restrictions on versions, and an indication of whether these required modules are
94 part of the standard Perl distribution, part of the module's distribution,
95 or must be installed separately.
96
97
98 =head1 INCOMPATIBILITIES
99
100 A list of any modules that this module cannot be used in conjunction with.
101 This may be due to name conflicts in the interface, or competition for
102 system or program resources, or due to internal limitations of Perl
103 (for example, many modules that use source code filters are mutually
104 incompatible).
105
106
107 =head1 BUGS AND LIMITATIONS
108
109 A list of known problems with the module, together with some indication of
110 whether they are likely to be fixed in an upcoming release.
111
112 Also a list of restrictions on the features the module does provide:
113 data types that cannot be handled, performance issues and the circumstances
114 in which they may arise, practical limitations on the size of data sets,
115 special cases that are not (yet) handled, etc.
116
117 The initial template usually just has:
118
119 There are no known bugs in this module.
120 Please report problems to <Maintainer name(s)> (<contact address>)
121 Patches are welcome.
122
123 =head1 AUTHOR
124
125 <Author name(s)> (<contact address>)
126
127
128
129 =head1 LICENCE AND COPYRIGHT
130
131 Copyright (c) <year> <copyright holder> (<contact address>). All rights reserved.
132
133 followed by whatever licence you wish to release it under.
134 For Perl code that is often just:
135
136 This module is free software; you can redistribute it and/or
137 modify it under the same terms as Perl itself. See L<perlartistic>.
138
139 This program is distributed in the hope that it will be useful,
140 but WITHOUT ANY WARRANTY; without even the implied warranty of
141 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
142