107 lines
3.0 KiB
Raku
107 lines
3.0 KiB
Raku
#!/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 two packed DNA bytes (eight bases)
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# and a character (A, C, G or T), returns how many times that character
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# occurs in that packed pair of bytes. Useful for quickly counting
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# character occurrences in long strings. The LUT is indexed first by
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# character (0 - 3) then by byte (0 - 2^16-1).
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#
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# See ebwt.h.
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#
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my @as = ();
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my @cs = ();
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my @gs = ();
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my @ts = ();
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# Compile character arrays
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my $i;
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for($i = 0; $i < (256*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 $b89 = ($i >> 8) & 3;
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my $b1011 = ($i >> 10) & 3;
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my $b1213 = ($i >> 12) & 3;
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my $b1415 = ($i >> 14) & 3;
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my $a = ($b01 == 0) + ($b23 == 0) + ($b45 == 0) + ($b67 == 0) +
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($b89 == 0) + ($b1011 == 0) + ($b1213 == 0) + ($b1415 == 0);
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my $c = ($b01 == 1) + ($b23 == 1) + ($b45 == 1) + ($b67 == 1) +
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($b89 == 1) + ($b1011 == 1) + ($b1213 == 1) + ($b1415 == 1);
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my $g = ($b01 == 2) + ($b23 == 2) + ($b45 == 2) + ($b67 == 2) +
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($b89 == 2) + ($b1011 == 2) + ($b1213 == 2) + ($b1415 == 2);
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my $t = ($b01 == 3) + ($b23 == 3) + ($b45 == 3) + ($b67 == 3) +
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($b89 == 3) + ($b1011 == 3) + ($b1213 == 3) + ($b1415 == 3);
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push @as, $a;
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push @cs, $c;
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push @gs, $g;
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push @ts, $t;
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}
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my $entsPerLine = 16;
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# Count occurrences in all 4 bit pairs
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print "uint8_t cCntLUT_16b_4[4][256*256] = {\n";
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# Print As array
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print "\t/* As */ {\n";
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for($i = 0; $i < (256*256); $i++) {
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print "\t\t" if(($i % $entsPerLine) == 0);
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print "$as[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t},\n";
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# Print Cs array
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print "\t/* Cs */ {\n";
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for($i = 0; $i < (256*256); $i++) {
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print "\t\t" if(($i % $entsPerLine) == 0);
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print "$cs[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t},\n";
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# Print Gs array
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print "\t/* Gs */ {\n";
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for($i = 0; $i < (256*256); $i++) {
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print "\t\t" if(($i % $entsPerLine) == 0);
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print "$gs[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t},\n";
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# Print Ts array
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print "\t/* Ts */ {\n";
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for($i = 0; $i < (256*256); $i++) {
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print "\t\t" if(($i % $entsPerLine) == 0);
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print "$ts[$i], ";
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print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
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}
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print "\t}\n";
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print "};\n";
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