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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,238 @@ | ||
| #!/usr/bin/perl -w | ||
|
|
||
| # | ||
| # Generate lookup table that, given a packed DNA byte (four bases) and | ||
| # a character (A, C, G or T), returns how many times that character | ||
| # occurs in that packed byte. Useful for quickly counting character | ||
| # occurrences in long strings. The LUT is indexed first by character | ||
| # (0-3) then by byte (0-255). | ||
| # | ||
| # Larger lookup tables are also possible, though they seem | ||
| # counterproductive. E.g., looking up eight bases at a time yields a | ||
| # 256K LUT, which doesn't fit in L1. A four-base LUT is 1KB, easily | ||
| # fitting in L1. | ||
| # | ||
| # See ebwt.h. | ||
| # | ||
|
|
||
| my @as4 = (), @as3 = (), @as2 = (), @as1 = (); | ||
| my @cs4 = (), @cs3 = (), @cs2 = (), @cs1 = (); | ||
| my @gs4 = (), @gs3 = (), @gs2 = (), @gs1 = (); | ||
| my @ts4 = (), @ts3 = (), @ts2 = (), @ts1 = (); | ||
|
|
||
| # Compile character arrays | ||
| my $i; | ||
| for($i = 0; $i < 256; $i++) { | ||
| my $b01 = ($i >> 0) & 3; | ||
| my $b23 = ($i >> 2) & 3; | ||
| my $b45 = ($i >> 4) & 3; | ||
| my $b67 = ($i >> 6) & 3; | ||
|
|
||
| my $a4 = ($b01 == 0) + ($b23 == 0) + ($b45 == 0) + ($b67 == 0); | ||
| my $c4 = ($b01 == 1) + ($b23 == 1) + ($b45 == 1) + ($b67 == 1); | ||
| my $g4 = ($b01 == 2) + ($b23 == 2) + ($b45 == 2) + ($b67 == 2); | ||
| my $t4 = ($b01 == 3) + ($b23 == 3) + ($b45 == 3) + ($b67 == 3); | ||
|
|
||
| push @as4, $a4; | ||
| push @cs4, $c4; | ||
| push @gs4, $g4; | ||
| push @ts4, $t4; | ||
|
|
||
| my $a3 = ($b01 == 0) + ($b23 == 0) + ($b45 == 0); | ||
| my $c3 = ($b01 == 1) + ($b23 == 1) + ($b45 == 1); | ||
| my $g3 = ($b01 == 2) + ($b23 == 2) + ($b45 == 2); | ||
| my $t3 = ($b01 == 3) + ($b23 == 3) + ($b45 == 3); | ||
|
|
||
| push @as3, $a3; | ||
| push @cs3, $c3; | ||
| push @gs3, $g3; | ||
| push @ts3, $t3; | ||
|
|
||
| my $a2 = ($b01 == 0) + ($b23 == 0); | ||
| my $c2 = ($b01 == 1) + ($b23 == 1); | ||
| my $g2 = ($b01 == 2) + ($b23 == 2); | ||
| my $t2 = ($b01 == 3) + ($b23 == 3); | ||
|
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||
| push @as2, $a2; | ||
| push @cs2, $c2; | ||
| push @gs2, $g2; | ||
| push @ts2, $t2; | ||
|
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||
| my $a1 = ($b01 == 0) + 0; | ||
| my $c1 = ($b01 == 1) + 0; | ||
| my $g1 = ($b01 == 2) + 0; | ||
| my $t1 = ($b01 == 3) + 0; | ||
|
|
||
| push @as1, $a1; | ||
| push @cs1, $c1; | ||
| push @gs1, $g1; | ||
| push @ts1, $t1; | ||
| } | ||
|
|
||
| my $entsPerLine = 16; | ||
|
|
||
| print "#include <stdint.h>\n\n"; | ||
| print "/* Generated by gen_lookup_tables.pl */\n\n"; | ||
|
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| # Count occurrences in all 4 bit pairs | ||
|
|
||
| print "uint8_t cCntLUT_4[4][4][256] = {\n"; | ||
| print "\t/* All 4 bit pairs */ {\n"; | ||
|
|
||
| # Print As array | ||
| print "\t\t/* As */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$as4[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Cs array | ||
| print "\t\t/* Cs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$cs4[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Gs array | ||
| print "\t\t/* Gs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$gs4[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Ts array | ||
| print "\t\t/* Ts */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$ts4[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| 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"; | ||
|
|
||
| # Print As array | ||
| print "\t\t/* As */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$as1[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Cs array | ||
| print "\t\t/* Cs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$cs1[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Gs array | ||
| print "\t\t/* Gs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$gs1[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Ts array | ||
| print "\t\t/* Ts */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$ts1[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t}\n\t},\n"; | ||
|
|
||
| # Count occurrences in low 2 bit pairs | ||
|
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||
| print "\t/* Least significant 2 bit pairs */ {\n"; | ||
|
|
||
| # Print As array | ||
| print "\t\t/* As */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$as2[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Cs array | ||
| print "\t\t/* Cs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$cs2[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Gs array | ||
| print "\t\t/* Gs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$gs2[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Ts array | ||
| print "\t\t/* Ts */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$ts2[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t}\n\t},\n"; | ||
|
|
||
| # Count occurrences in low 3 bit pairs | ||
|
|
||
| print "\t/* Least significant 3 bit pairs */ {\n"; | ||
|
|
||
| # Print As array | ||
| print "\t\t/* As */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$as3[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Cs array | ||
| print "\t\t/* Cs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$cs3[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Gs array | ||
| print "\t\t/* Gs */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$gs3[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t},\n"; | ||
|
|
||
| # Print Ts array | ||
| print "\t\t/* Ts */ {\n"; | ||
| for($i = 0; $i < 256; $i++) { | ||
| print "\t\t\t" if(($i % $entsPerLine) == 0); | ||
| print "$ts3[$i], "; | ||
| print "\n" if(($i % $entsPerLine) == ($entsPerLine-1)); | ||
| } | ||
| print "\t\t}\n\t}\n"; | ||
|
|
||
| print "};\n"; |
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