81 lines
2.0 KiB
Perl
81 lines
2.0 KiB
Perl
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#!/usr/bin/perl -w
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#
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# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
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#
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# This file is part of Bowtie 2.
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#
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# Bowtie 2 is free software: you can redistribute it and/or modify
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# it under the terms of the GNU General Public License as published by
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# the Free Software Foundation, either version 3 of the License, or
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# (at your option) any later version.
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#
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# Bowtie 2 is distributed in the hope that it will be useful,
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# but WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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# GNU General Public License for more details.
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#
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# You should have received a copy of the GNU General Public License
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# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
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#
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use warnings;
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use strict;
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sub log10($) {
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return log(shift) / log(10.0);
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}
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sub round {
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my($number) = shift;
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return int($number + .5 * ($number <=> 0));
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}
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# Convert from solexa qual to probability of miscall
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sub phredToP($) {
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my $sol = shift;
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my $p = (10.0 ** (($sol) / -10.0));
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($p >= 0.0 && $p <= 1.0) || die "Bad prob: $p, from sol $sol";
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return $p;
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}
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# Convert from phred qual to probability of miscall
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sub solToP($) {
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my $phred = shift;
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my $x = (10.0 ** (($phred) / -10.0));
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my $p = $x / (1.0 + $x);
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($p >= 0.0 && $p <= 1.0) || die "Bad prob: $p, from x $x, phred $phred";
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return $p;
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}
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# Convert from probability of miscall to phred qual
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sub pToPhred($) {
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my $p = shift;
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($p >= 0.0 && $p <= 1.0) || die "Bad prob: $p";
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return round(-10.0 * log10($p));
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}
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# Convert from probability of miscall to solexa qual
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sub pToSol($) {
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my $p = shift;
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($p >= 0.0 && $p <= 1.0) || die "Bad prob: $p";
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return 0 if($p == 1.0);
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return round(-10.0 * log10($p / (1.0 - $p)));
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}
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# Print conversion table from Phred to Solexa
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print "uint8_t solToPhred[] = {";
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my $cols = 10;
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my $cnt = 0;
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for(my $i = -10; $i < 256; $i++) {
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# Solexa qual = $i
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my $p = solToP($i);
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my $ph = pToPhred($p);
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print "\n\t/* $i */ " if($cnt == 0);
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$cnt++;
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$cnt = 0 if($cnt == 10);
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print "$ph";
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print ", " if($i < 255);
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}
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print "\n};\n";
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