107 lines
3.0 KiB
Perl
107 lines
3.0 KiB
Perl
|
#!/usr/bin/perl -w
|
||
|
|
|
||
|
|
#
|
||
|
|
# Copyright 2011, Ben Langmead <langmea@cs.jhu.edu>
|
||
|
|
#
|
||
|
|
# This file is part of Bowtie 2.
|
||
|
|
#
|
||
|
|
# Bowtie 2 is free software: you can redistribute it and/or modify
|
||
|
|
# it under the terms of the GNU General Public License as published by
|
||
|
|
# the Free Software Foundation, either version 3 of the License, or
|
||
|
|
# (at your option) any later version.
|
||
|
|
#
|
||
|
|
# Bowtie 2 is distributed in the hope that it will be useful,
|
||
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||
|
|
# GNU General Public License for more details.
|
||
|
|
#
|
||
|
|
# You should have received a copy of the GNU General Public License
|
||
|
|
# along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
|
||
|
|
#
|
||
|
|
|
||
|
|
#
|
||
|
|
# Generate lookup table that, given two packed DNA bytes (eight bases)
|
||
|
|
# and a character (A, C, G or T), returns how many times that character
|
||
|
|
# occurs in that packed pair of bytes. Useful for quickly counting
|
||
|
|
# character occurrences in long strings. The LUT is indexed first by
|
||
|
|
# character (0 - 3) then by byte (0 - 2^16-1).
|
||
|
|
#
|
||
|
|
# See ebwt.h.
|
||
|
|
#
|
||
|
|
|
||
|
|
my @as = ();
|
||
|
|
my @cs = ();
|
||
|
|
my @gs = ();
|
||
|
|
my @ts = ();
|
||
|
|
|
||
|
|
# Compile character arrays
|
||
|
|
my $i;
|
||
|
|
for($i = 0; $i < (256*256); $i++) {
|
||
|
|
|
||
|
|
my $b01 = ($i >> 0) & 3;
|
||
|
|
my $b23 = ($i >> 2) & 3;
|
||
|
|
my $b45 = ($i >> 4) & 3;
|
||
|
|
my $b67 = ($i >> 6) & 3;
|
||
|
|
my $b89 = ($i >> 8) & 3;
|
||
|
|
my $b1011 = ($i >> 10) & 3;
|
||
|
|
my $b1213 = ($i >> 12) & 3;
|
||
|
|
my $b1415 = ($i >> 14) & 3;
|
||
|
|
|
||
|
|
my $a = ($b01 == 0) + ($b23 == 0) + ($b45 == 0) + ($b67 == 0) +
|
||
|
|
($b89 == 0) + ($b1011 == 0) + ($b1213 == 0) + ($b1415 == 0);
|
||
|
|
my $c = ($b01 == 1) + ($b23 == 1) + ($b45 == 1) + ($b67 == 1) +
|
||
|
|
($b89 == 1) + ($b1011 == 1) + ($b1213 == 1) + ($b1415 == 1);
|
||
|
|
my $g = ($b01 == 2) + ($b23 == 2) + ($b45 == 2) + ($b67 == 2) +
|
||
|
|
($b89 == 2) + ($b1011 == 2) + ($b1213 == 2) + ($b1415 == 2);
|
||
|
|
my $t = ($b01 == 3) + ($b23 == 3) + ($b45 == 3) + ($b67 == 3) +
|
||
|
|
($b89 == 3) + ($b1011 == 3) + ($b1213 == 3) + ($b1415 == 3);
|
||
|
|
|
||
|
|
push @as, $a;
|
||
|
|
push @cs, $c;
|
||
|
|
push @gs, $g;
|
||
|
|
push @ts, $t;
|
||
|
|
}
|
||
|
|
|
||
|
|
my $entsPerLine = 16;
|
||
|
|
|
||
|
|
# Count occurrences in all 4 bit pairs
|
||
|
|
|
||
|
|
print "uint8_t cCntLUT_16b_4[4][256*256] = {\n";
|
||
|
|
|
||
|
|
# Print As array
|
||
|
|
print "\t/* As */ {\n";
|
||
|
|
for($i = 0; $i < (256*256); $i++) {
|
||
|
|
print "\t\t" if(($i % $entsPerLine) == 0);
|
||
|
|
print "$as[$i], ";
|
||
|
|
print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
|
||
|
|
}
|
||
|
|
print "\t},\n";
|
||
|
|
|
||
|
|
# Print Cs array
|
||
|
|
print "\t/* Cs */ {\n";
|
||
|
|
for($i = 0; $i < (256*256); $i++) {
|
||
|
|
print "\t\t" if(($i % $entsPerLine) == 0);
|
||
|
|
print "$cs[$i], ";
|
||
|
|
print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
|
||
|
|
}
|
||
|
|
print "\t},\n";
|
||
|
|
|
||
|
|
# Print Gs array
|
||
|
|
print "\t/* Gs */ {\n";
|
||
|
|
for($i = 0; $i < (256*256); $i++) {
|
||
|
|
print "\t\t" if(($i % $entsPerLine) == 0);
|
||
|
|
print "$gs[$i], ";
|
||
|
|
print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
|
||
|
|
}
|
||
|
|
print "\t},\n";
|
||
|
|
|
||
|
|
# Print Ts array
|
||
|
|
print "\t/* Ts */ {\n";
|
||
|
|
for($i = 0; $i < (256*256); $i++) {
|
||
|
|
print "\t\t" if(($i % $entsPerLine) == 0);
|
||
|
|
print "$ts[$i], ";
|
||
|
|
print "\n" if(($i % $entsPerLine) == ($entsPerLine-1));
|
||
|
|
}
|
||
|
|
print "\t}\n";
|
||
|
|
print "};\n";
|