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#!/usr/bin/perl
# filter of help2man output
use strict;
use warnings;
while ( <STDIN> ) {
#multiline regex
undef $/;
# remove colon from the name
s/(^\.SH\sDESCRIPTION\n.*\.IP\n)(cat)/$2/gmxs;
s/(^\.PP\n)(Input\soptions.*)/.SH OPTIONS\n.SS $2/gmxs;
s/(^Batch\smode\s\(default\s=\s2\)\n)(Mode.*)/$1\n $2/gmxs;
s/(^\.TP\n)(0)(\n)(see\snote.*)/ $2 $4/gmxs;
s/(^\.TP\n)(1)(\n)(see\snote.*)/ $2 $4/gmxs;
s/(^\.TP\n)(\(default\))(\n)(2\s{6}see\snote.*)/ $2 $4/gmxs;
s/(^3\s{6}see\snote.*)/ $1/gmxs;
s/(^4\s{6}see\snote.*)/ $1/gmxs;
s/(^5\s{6}expand\s.*)/ $1/gmxs;
# lineup "-f format" option of gmap
s/(under\sOutput\stypes\)\:\n)(.*)\.PP\n/
my $q = $1;
my $p = $2;
$p =~ s"(\,\n)"$1 "gmxs;
$p = $q.' '.$p;
/egmsx;
#gsnap aligning
s/(^\.TP\n)(\(default\))(\n\s+)(4\s{6}see\snote.*)/ $2 $4/gmxs;
s/(^\.TP\n)(2)(\n)(see\snote.*)/ $2 $4/gmxs;
s/(^\.TP\n)(3)(\n)(see\snote.*)/ $2 $4/gmxs;
s/(^5\s{6}see\snote\s.*)/ $1/gmxs;
s/(^Examples:\n\.TP)/\.TP\n$1/gmsx;
s/(.*be\schanged)\n\.TP\n(by\sproviding.*)/$1 $2/gmsx;
#fix gmap_build header
s/(^\.SH\sDESCRIPTION\n)Unknown.*\.PP/$1/gmsx;
print;
}
print "\n\.TP\nOther tools of GMAP suite are located in \/usr\/lib\/gmap";
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