258 lines
6.5 KiB
Perl
258 lines
6.5 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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#
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# Generate lookup table that, given a packed DNA byte (four bases) and
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# a character (A, C, G or T), returns how many times that character
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# occurs in that packed byte. Useful for quickly counting character
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# occurrences in long strings. The LUT is indexed first by character
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# (0-3) then by byte (0-255).
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#
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# Larger lookup tables are also possible, though they seem
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# counterproductive. E.g., looking up eight bases at a time yields a
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# 256K LUT, which doesn't fit in L1. A four-base LUT is 1KB, easily
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# fitting in L1.
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#
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# See ebwt.h.
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#
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my @as4 = (), @as3 = (), @as2 = (), @as1 = ();
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my @cs4 = (), @cs3 = (), @cs2 = (), @cs1 = ();
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my @gs4 = (), @gs3 = (), @gs2 = (), @gs1 = ();
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my @ts4 = (), @ts3 = (), @ts2 = (), @ts1 = ();
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# Compile character arrays
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my $i;
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for($i = 0; $i < 256; $i++) {
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my $b01 = ($i >> 0) & 3;
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my $b23 = ($i >> 2) & 3;
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my $b45 = ($i >> 4) & 3;
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my $b67 = ($i >> 6) & 3;
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my $a4 = ($b01 == 0) + ($b23 == 0) + ($b45 == 0) + ($b67 == 0);
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my $c4 = ($b01 == 1) + ($b23 == 1) + ($b45 == 1) + ($b67 == 1);
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my $g4 = ($b01 == 2) + ($b23 == 2) + ($b45 == 2) + ($b67 == 2);
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my $t4 = ($b01 == 3) + ($b23 == 3) + ($b45 == 3) + ($b67 == 3);
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push @as4, $a4;
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push @cs4, $c4;
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push @gs4, $g4;
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push @ts4, $t4;
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my $a3 = ($b01 == 0) + ($b23 == 0) + ($b45 == 0);
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my $c3 = ($b01 == 1) + ($b23 == 1) + ($b45 == 1);
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my $g3 = ($b01 == 2) + ($b23 == 2) + ($b45 == 2);
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my $t3 = ($b01 == 3) + ($b23 == 3) + ($b45 == 3);
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push @as3, $a3;
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push @cs3, $c3;
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push @gs3, $g3;
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push @ts3, $t3;
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my $a2 = ($b01 == 0) + ($b23 == 0);
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my $c2 = ($b01 == 1) + ($b23 == 1);
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my $g2 = ($b01 == 2) + ($b23 == 2);
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my $t2 = ($b01 == 3) + ($b23 == 3);
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push @as2, $a2;
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push @cs2, $c2;
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push @gs2, $g2;
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push @ts2, $t2;
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my $a1 = ($b01 == 0) + 0;
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my $c1 = ($b01 == 1) + 0;
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my $g1 = ($b01 == 2) + 0;
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my $t1 = ($b01 == 3) + 0;
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push @as1, $a1;
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push @cs1, $c1;
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push @gs1, $g1;
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push @ts1, $t1;
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}
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my $entsPerLine = 16;
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print "#include <stdint.h>\n\n";
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print "/* Generated by gen_lookup_tables.pl */\n\n";
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# Count occurrences in all 4 bit pairs
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print "uint8_t cCntLUT_4[4][4][256] = {\n";
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print "\t/* All 4 bit pairs */ {\n";
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# Print As array
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print "\t\t/* As */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$as4[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Cs array
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print "\t\t/* Cs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$cs4[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Gs array
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print "\t\t/* Gs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$gs4[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Ts array
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print "\t\t/* Ts */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$ts4[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t}\n\t},\n";
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# Count occurrences in low 1 bit pair
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print "\t/* Least significant 1 bit pair */ {\n";
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# Print As array
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print "\t\t/* As */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$as1[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Cs array
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print "\t\t/* Cs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$cs1[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Gs array
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print "\t\t/* Gs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$gs1[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Ts array
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print "\t\t/* Ts */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$ts1[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t}\n\t},\n";
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# Count occurrences in low 2 bit pairs
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print "\t/* Least significant 2 bit pairs */ {\n";
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# Print As array
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print "\t\t/* As */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$as2[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Cs array
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print "\t\t/* Cs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$cs2[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Gs array
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print "\t\t/* Gs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$gs2[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Ts array
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print "\t\t/* Ts */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$ts2[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t}\n\t},\n";
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# Count occurrences in low 3 bit pairs
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print "\t/* Least significant 3 bit pairs */ {\n";
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# Print As array
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print "\t\t/* As */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$as3[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Cs array
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print "\t\t/* Cs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$cs3[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Gs array
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print "\t\t/* Gs */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$gs3[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t},\n";
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# Print Ts array
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print "\t\t/* Ts */ {\n";
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for($i = 0; $i < 256; $i++) {
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print "\t\t\t" if(($i % $entsPerLine) == 0);
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print "$ts3[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t\t}\n\t}\n";
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print "};\n";
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