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#!/usr/bin/perl
# filter of help2man output
use strict;
use warnings;
while ( <STDIN> ) {
#multiline regex
undef $/;
# substitude unrecognized version string with the version
$_ =~ s/(\.SH\sDESCRIPTION\n)(No\sinput\ssequence.*?)(\n)/$1\.TP$3/gxms;
$_ =~ s/(\*{3}\n)(Options):\n\.TP/$1.'.SH '.uc($2)/gmsex;
$_ =~ s/(\.PP\n)(Options)(\s.*?):(\n)/$1.'.SH '.uc($2).$3.$4/msex;
$_ =~ s{(\.IP\n)(Input|Presets|Alignment|Scoring|Reporting|
Effort|Paired-end|Output|Performance|Other)(:\n)(\.TP|\.HP\n)}
{.SS $2$3$4}gmsx;
$_ =~ s/(\.TP\n)(Presets:)\n/\.SS $2\n/xms;
$_ =~ s{(\(Note:\sfor.*?\.)(\n\.IP)}{
my ($p,$q) = ($1,$2);
$p =~ s/(\n)/$1 /gxms;
$p = ' '.$p.$q;
}msex;
$_ =~ s/.*(\soutput\sfile\sspecified\!|No\sindex\sname\sgiven\!)//g;
$_ =~ s/\(ERR\):.*$//g;
$_ =~ s/(Usage:\n\.IP)/.SH\nUSAGE/g;
$_ =~ s/\*{3}\sWarning.*\sinstead\.//gxms;
print $_;
}
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