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encode.c
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#include <stdio.h>
#include "encode.h"
const uint8_t nt256char_to_nt4_table[128] = {
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 0, 1, 64, 1, 1, 1,128, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1,192, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
};
const char nt4_to_nt256char_table[256] = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";
const int8_t nt4_to_nt256int8_table[256] = {
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3
};
const uint8_t nt4_to_nt16_table[256] = {
16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128
};
const uint8_t nt4_rev_table[256] = {
255,191,127, 63,239,175,111, 47,223,159, 95, 31,207,143, 79, 15,
251,187,123, 59,235,171,107, 43,219,155, 91, 27,203,139, 75, 11,
247,183,119, 55,231,167,103, 39,215,151, 87, 23,199,135, 71, 7,
243,179,115, 51,227,163, 99, 35,211,147, 83, 19,195,131, 67, 3,
254,190,126, 62,238,174,110, 46,222,158, 94, 30,206,142, 78, 14,
250,186,122, 58,234,170,106, 42,218,154, 90, 26,202,138, 74, 10,
246,182,118, 54,230,166,102, 38,214,150, 86, 22,198,134, 70, 6,
242,178,114, 50,226,162, 98, 34,210,146, 82, 18,194,130, 66, 2,
253,189,125, 61,237,173,109, 45,221,157, 93, 29,205,141, 77, 13,
249,185,121, 57,233,169,105, 41,217,153, 89, 25,201,137, 73, 9,
245,181,117, 53,229,165,101, 37,213,149, 85, 21,197,133, 69, 5,
241,177,113, 49,225,161, 97, 33,209,145, 81, 17,193,129, 65, 1,
252,188,124, 60,236,172,108, 44,220,156, 92, 28,204,140, 76, 12,
248,184,120, 56,232,168,104, 40,216,152, 88, 24,200,136, 72, 8,
244,180,116, 52,228,164,100, 36,212,148, 84, 20,196,132, 68, 4,
240,176,112, 48,224,160, 96, 32,208,144, 80, 16,192,128, 64, 0
};
/* similar to bam_nt16_table from samtools' bam_import.c
* except that here uses upper four bits.
*
* Note that this table contains several conversion
* '1','2','3','4' => 1,2,4,8
* 'A','C','G','T', 'N' => 1,2,4,8,15
* */
const uint8_t nt256char_to_nt16_table[128] = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 16, 32, 64,128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 16, 0, 32, 0, 0, 0, 64, 0, 0, 0, 0, 0, 0,240, 0,
0, 0, 0, 0,128, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
const char nt16_to_nt256char_table[256]="================AAAAAAAAAAAAAAAACCCCCCCCCCCCCCCC================GGGGGGGGGGGGGGGG================================================TTTTTTTTTTTTTTTT================================================================================================NNNNNNNNNNNNNNNN";
const int8_t nt16_to_nt256int8_table[256]={
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,
4,4,4,4,4,4,4,4,4,4,4,4,4,4,4,4
};
const uint8_t nt16_rev_table[256] = {
0,128, 64,192, 32,160, 96,224, 16,144, 80,208, 48,176,112,240,
8,136, 72,200, 40,168,104,232, 24,152, 88,216, 56,184,120,248,
4,132, 68,196, 36,164,100,228, 20,148, 84,212, 52,180,116,244,
12,140, 76,204, 44,172,108,236, 28,156, 92,220, 60,188,124,252,
2,130, 66,194, 34,162, 98,226, 18,146, 82,210, 50,178,114,242,
10,138, 74,202, 42,170,106,234, 26,154, 90,218, 58,186,122,250,
6,134, 70,198, 38,166,102,230, 22,150, 86,214, 54,182,118,246,
14,142, 78,206, 46,174,110,238, 30,158, 94,222, 62,190,126,254,
1,129, 65,193, 33,161, 97,225, 17,145, 81,209, 49,177,113,241,
9,137, 73,201, 41,169,105,233, 25,153, 89,217, 57,185,121,249,
5,133, 69,197, 37,165,101,229, 21,149, 85,213, 53,181,117,245,
13,141, 77,205, 45,173,109,237, 29,157, 93,221, 61,189,125,253,
3,131, 67,195, 35,163, 99,227, 19,147, 83,211, 51,179,115,243,
11,139, 75,203, 43,171,107,235, 27,155, 91,219, 59,187,123,251,
7,135, 71,199, 39,167,103,231, 23,151, 87,215, 55,183,119,247,
15,143, 79,207, 47,175,111,239, 31,159, 95,223, 63,191,127,255,
};
const char nt256int8_to_nt256char_table[5] = "ACGTN";
const int8_t nt256char_to_nt256int8_table[128] = {
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4
};
const uint8_t nt256char_to_nt8_table[256] = {
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160, 0,160, 32,160,160,160,192,160,160,160,160,160,160,160,160,
160,160,160,160,224,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160
};
const char nt8_to_nt256char_table[256] = "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";
const uint8_t nt8_rev_table[256] = {
224,224,224,224,224,224,224,224,224,224,224,224,224,224,224,224,
224,224,224,224,224,224,224,224,224,224,224,224,224,224,224,224,
192,192,192,192,192,192,192,192,192,192,192,192,192,192,192,192,
192,192,192,192,192,192,192,192,192,192,192,192,192,192,192,192,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,160,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,
128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,128,
96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96,
96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64, 64,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
};
const char nt256char_rev_table[128] = "NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTNGNNNCNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN";
const char nt4_to_nt3_ct_table[4] = {0,2,1,2}; /* A [CT] G [CT] */
const char nt4_to_nt3_ga_table[4] = {0,1,0,2}; /* [AG] C [AG] T */
/* switch 5 bases from a 4-base space representation to 3-base space (CT degenerate) representation
4**5 (1024) to 3**5 (243, fit in one byte) */
const uint8_t fivebase43CT_switch[1024] = {
0, 2, 1, 2, 6, 8, 7, 8, 3, 5, 4, 5, 6, 8, 7, 8,
18, 20, 19, 20, 24, 26, 25, 26, 21, 23, 22, 23, 24, 26, 25, 26,
9, 11, 10, 11, 15, 17, 16, 17, 12, 14, 13, 14, 15, 17, 16, 17,
18, 20, 19, 20, 24, 26, 25, 26, 21, 23, 22, 23, 24, 26, 25, 26,
54, 56, 55, 56, 60, 62, 61, 62, 57, 59, 58, 59, 60, 62, 61, 62,
72, 74, 73, 74, 78, 80, 79, 80, 75, 77, 76, 77, 78, 80, 79, 80,
63, 65, 64, 65, 69, 71, 70, 71, 66, 68, 67, 68, 69, 71, 70, 71,
72, 74, 73, 74, 78, 80, 79, 80, 75, 77, 76, 77, 78, 80, 79, 80,
27, 29, 28, 29, 33, 35, 34, 35, 30, 32, 31, 32, 33, 35, 34, 35,
45, 47, 46, 47, 51, 53, 52, 53, 48, 50, 49, 50, 51, 53, 52, 53,
36, 38, 37, 38, 42, 44, 43, 44, 39, 41, 40, 41, 42, 44, 43, 44,
45, 47, 46, 47, 51, 53, 52, 53, 48, 50, 49, 50, 51, 53, 52, 53,
54, 56, 55, 56, 60, 62, 61, 62, 57, 59, 58, 59, 60, 62, 61, 62,
72, 74, 73, 74, 78, 80, 79, 80, 75, 77, 76, 77, 78, 80, 79, 80,
63, 65, 64, 65, 69, 71, 70, 71, 66, 68, 67, 68, 69, 71, 70, 71,
72, 74, 73, 74, 78, 80, 79, 80, 75, 77, 76, 77, 78, 80, 79, 80,
162,164,163,164,168,170,169,170,165,167,166,167,168,170,169,170,
180,182,181,182,186,188,187,188,183,185,184,185,186,188,187,188,
171,173,172,173,177,179,178,179,174,176,175,176,177,179,178,179,
180,182,181,182,186,188,187,188,183,185,184,185,186,188,187,188,
216,218,217,218,222,224,223,224,219,221,220,221,222,224,223,224,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
225,227,226,227,231,233,232,233,228,230,229,230,231,233,232,233,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
189,191,190,191,195,197,196,197,192,194,193,194,195,197,196,197,
207,209,208,209,213,215,214,215,210,212,211,212,213,215,214,215,
198,200,199,200,204,206,205,206,201,203,202,203,204,206,205,206,
207,209,208,209,213,215,214,215,210,212,211,212,213,215,214,215,
216,218,217,218,222,224,223,224,219,221,220,221,222,224,223,224,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
225,227,226,227,231,233,232,233,228,230,229,230,231,233,232,233,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
81, 83, 82, 83, 87, 89, 88, 89, 84, 86, 85, 86, 87, 89, 88, 89,
99,101,100,101,105,107,106,107,102,104,103,104,105,107,106,107,
90, 92, 91, 92, 96, 98, 97, 98, 93, 95, 94, 95, 96, 98, 97, 98,
99,101,100,101,105,107,106,107,102,104,103,104,105,107,106,107,
135,137,136,137,141,143,142,143,138,140,139,140,141,143,142,143,
153,155,154,155,159,161,160,161,156,158,157,158,159,161,160,161,
144,146,145,146,150,152,151,152,147,149,148,149,150,152,151,152,
153,155,154,155,159,161,160,161,156,158,157,158,159,161,160,161,
108,110,109,110,114,116,115,116,111,113,112,113,114,116,115,116,
126,128,127,128,132,134,133,134,129,131,130,131,132,134,133,134,
117,119,118,119,123,125,124,125,120,122,121,122,123,125,124,125,
126,128,127,128,132,134,133,134,129,131,130,131,132,134,133,134,
135,137,136,137,141,143,142,143,138,140,139,140,141,143,142,143,
153,155,154,155,159,161,160,161,156,158,157,158,159,161,160,161,
144,146,145,146,150,152,151,152,147,149,148,149,150,152,151,152,
153,155,154,155,159,161,160,161,156,158,157,158,159,161,160,161,
162,164,163,164,168,170,169,170,165,167,166,167,168,170,169,170,
180,182,181,182,186,188,187,188,183,185,184,185,186,188,187,188,
171,173,172,173,177,179,178,179,174,176,175,176,177,179,178,179,
180,182,181,182,186,188,187,188,183,185,184,185,186,188,187,188,
216,218,217,218,222,224,223,224,219,221,220,221,222,224,223,224,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
225,227,226,227,231,233,232,233,228,230,229,230,231,233,232,233,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
189,191,190,191,195,197,196,197,192,194,193,194,195,197,196,197,
207,209,208,209,213,215,214,215,210,212,211,212,213,215,214,215,
198,200,199,200,204,206,205,206,201,203,202,203,204,206,205,206,
207,209,208,209,213,215,214,215,210,212,211,212,213,215,214,215,
216,218,217,218,222,224,223,224,219,221,220,221,222,224,223,224,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
225,227,226,227,231,233,232,233,228,230,229,230,231,233,232,233,
234,236,235,236,240,242,241,242,237,239,238,239,240,242,241,242,
};
const uint8_t fivebase43GA_switch[1024] = {
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
9, 10, 9, 11, 12, 13, 12, 14, 9, 10, 9, 11, 15, 16, 15, 17,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
18, 19, 18, 20, 21, 22, 21, 23, 18, 19, 18, 20, 24, 25, 24, 26,
27, 28, 27, 29, 30, 31, 30, 32, 27, 28, 27, 29, 33, 34, 33, 35,
36, 37, 36, 38, 39, 40, 39, 41, 36, 37, 36, 38, 42, 43, 42, 44,
27, 28, 27, 29, 30, 31, 30, 32, 27, 28, 27, 29, 33, 34, 33, 35,
45, 46, 45, 47, 48, 49, 48, 50, 45, 46, 45, 47, 51, 52, 51, 53,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
9, 10, 9, 11, 12, 13, 12, 14, 9, 10, 9, 11, 15, 16, 15, 17,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
18, 19, 18, 20, 21, 22, 21, 23, 18, 19, 18, 20, 24, 25, 24, 26,
54, 55, 54, 56, 57, 58, 57, 59, 54, 55, 54, 56, 60, 61, 60, 62,
63, 64, 63, 65, 66, 67, 66, 68, 63, 64, 63, 65, 69, 70, 69, 71,
54, 55, 54, 56, 57, 58, 57, 59, 54, 55, 54, 56, 60, 61, 60, 62,
72, 73, 72, 74, 75, 76, 75, 77, 72, 73, 72, 74, 78, 79, 78, 80,
81, 82, 81, 83, 84, 85, 84, 86, 81, 82, 81, 83, 87, 88, 87, 89,
90, 91, 90, 92, 93, 94, 93, 95, 90, 91, 90, 92, 96, 97, 96, 98,
81, 82, 81, 83, 84, 85, 84, 86, 81, 82, 81, 83, 87, 88, 87, 89,
99,100, 99,101,102,103,102,104, 99,100, 99,101,105,106,105,107,
108,109,108,110,111,112,111,113,108,109,108,110,114,115,114,116,
117,118,117,119,120,121,120,122,117,118,117,119,123,124,123,125,
108,109,108,110,111,112,111,113,108,109,108,110,114,115,114,116,
126,127,126,128,129,130,129,131,126,127,126,128,132,133,132,134,
81, 82, 81, 83, 84, 85, 84, 86, 81, 82, 81, 83, 87, 88, 87, 89,
90, 91, 90, 92, 93, 94, 93, 95, 90, 91, 90, 92, 96, 97, 96, 98,
81, 82, 81, 83, 84, 85, 84, 86, 81, 82, 81, 83, 87, 88, 87, 89,
99,100, 99,101,102,103,102,104, 99,100, 99,101,105,106,105,107,
135,136,135,137,138,139,138,140,135,136,135,137,141,142,141,143,
144,145,144,146,147,148,147,149,144,145,144,146,150,151,150,152,
135,136,135,137,138,139,138,140,135,136,135,137,141,142,141,143,
153,154,153,155,156,157,156,158,153,154,153,155,159,160,159,161,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
9, 10, 9, 11, 12, 13, 12, 14, 9, 10, 9, 11, 15, 16, 15, 17,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
18, 19, 18, 20, 21, 22, 21, 23, 18, 19, 18, 20, 24, 25, 24, 26,
27, 28, 27, 29, 30, 31, 30, 32, 27, 28, 27, 29, 33, 34, 33, 35,
36, 37, 36, 38, 39, 40, 39, 41, 36, 37, 36, 38, 42, 43, 42, 44,
27, 28, 27, 29, 30, 31, 30, 32, 27, 28, 27, 29, 33, 34, 33, 35,
45, 46, 45, 47, 48, 49, 48, 50, 45, 46, 45, 47, 51, 52, 51, 53,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
9, 10, 9, 11, 12, 13, 12, 14, 9, 10, 9, 11, 15, 16, 15, 17,
0, 1, 0, 2, 3, 4, 3, 5, 0, 1, 0, 2, 6, 7, 6, 8,
18, 19, 18, 20, 21, 22, 21, 23, 18, 19, 18, 20, 24, 25, 24, 26,
54, 55, 54, 56, 57, 58, 57, 59, 54, 55, 54, 56, 60, 61, 60, 62,
63, 64, 63, 65, 66, 67, 66, 68, 63, 64, 63, 65, 69, 70, 69, 71,
54, 55, 54, 56, 57, 58, 57, 59, 54, 55, 54, 56, 60, 61, 60, 62,
72, 73, 72, 74, 75, 76, 75, 77, 72, 73, 72, 74, 78, 79, 78, 80,
162,163,162,164,165,166,165,167,162,163,162,164,168,169,168,170,
171,172,171,173,174,175,174,176,171,172,171,173,177,178,177,179,
162,163,162,164,165,166,165,167,162,163,162,164,168,169,168,170,
180,181,180,182,183,184,183,185,180,181,180,182,186,187,186,188,
189,190,189,191,192,193,192,194,189,190,189,191,195,196,195,197,
198,199,198,200,201,202,201,203,198,199,198,200,204,205,204,206,
189,190,189,191,192,193,192,194,189,190,189,191,195,196,195,197,
207,208,207,209,210,211,210,212,207,208,207,209,213,214,213,215,
162,163,162,164,165,166,165,167,162,163,162,164,168,169,168,170,
171,172,171,173,174,175,174,176,171,172,171,173,177,178,177,179,
162,163,162,164,165,166,165,167,162,163,162,164,168,169,168,170,
180,181,180,182,183,184,183,185,180,181,180,182,186,187,186,188,
216,217,216,218,219,220,219,221,216,217,216,218,222,223,222,224,
225,226,225,227,228,229,228,230,225,226,225,227,231,232,231,233,
216,217,216,218,219,220,219,221,216,217,216,218,222,223,222,224,
234,235,234,236,237,238,237,239,234,235,234,236,240,241,240,242,
};
#ifdef MAIN_PRINT_CODING_TABLE
/* gcc lib/utils/encode.c -DMAIN_PRINT_CODING_TABLE -Iinclude */
int main() {
int i;
uint8_t j;
printf("fivebase 4base space => 3base CT space\n");
uint16_t k, k4, k3;
for (k=0; k<1024; k++) {
k3 = 0; k4 = k;
for (i=8; i>=0; i-=2) {
k3 *= 3;
k3 += nt4_to_nt3_ct_table[(k4>>i)&0x3];
}
printf("%3u,", k3);
if (((k+1)&0xf)==0) printf("\n");
}
printf("\n");
printf("fivebase 4base space => 3base GA space\n");
for (k=0; k<1024; k++) {
k3 = 0; k4 = k;
for (i=8; i>=0; i-=2) {
k3 *= 3;
k3 += nt4_to_nt3_ga_table[(k4>>i)&0x3];
}
printf("%3u,", k3);
if (((k+1)&0xf)==0) printf("\n");
}
printf("\n");
printf("nt256char => nt4\n");
for (i=0; i<128; i++) {
if (i == 'A') printf("%3d,", 0);
else if (i == 'C') printf("%3d,", 0x40);
else if (i == 'G') printf("%3d,", 0x80);
else if (i == 'T') printf("%3d,", 0xC0);
else printf("%3d,", 1);
if (((i+1) & 0xf) == 0) printf("\n");
}
printf("\n\nnt4 => nt256char\n");
for (i=0; i<256; i++) {
if ((i & 0xC0) == 0) putchar('A');
else if ((i & 0xC0) == 0x40) putchar('C');
else if ((i & 0xC0) == 0x80) putchar('G');
else if ((i & 0xC0) == 0xC0) putchar('T');
else putchar('N');
}
printf("\n\nnt4 => nt256int8\n");
for (i=0; i<256; i++) {
if ((i & 0xC0) == 0) printf("%d,", 0);
else if ((i & 0xC0) == 0x40) printf("%d,", 1);
else if ((i & 0xC0) == 0x80) printf("%d,", 2);
else if ((i & 0xC0) == 0xC0) printf("%d,", 3);
else printf("%d,", 4);
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n\nnt4 rev");
for (i=0; i<256; i++) {
j=i;
j=((j & 0xF0)>>4 | (j & 0x0F)<<4);
j=((j & 0xCC)>>2 | (j & 0x33)<<2);
printf("%3u,", (uint8_t) ~j);
if (((i+1) & 0xf) == 0) printf("\n");
}
printf("\n\nnt4 => nt16\n");
for (i=0; i<256; i++) {
if ((i & 0xC0) == 0) printf("%3d,", 0x10);
else if ((i & 0xC0) == 0x40) printf("%3d,", 0x20);
else if ((i & 0xC0) == 0x80) printf("%3d,", 0x40);
else if ((i & 0xC0) == 0xC0) printf("%3d,", 0x80);
else printf("%d,", 0);
if (((i+1) & 0xf) == 0) printf("\n");
}
printf("\n\nnt256char => nt16\n");
for (i=0; i<128; i++) {
if (i == 'A') printf("%3d,", 0x10);
else if (i == 'C') printf("%3d,", 0x20);
else if (i == 'G') printf("%3d,", 0x40);
else if (i == 'T') printf("%3d,", 0x80);
else if (i == 'N') printf("%3d,", 0xF0);
else if (i == '1') printf("%3d,", 0x10);
else if (i == '2') printf("%3d,", 0x20);
else if (i == '3') printf("%3d,", 0x40);
else if (i == '4') printf("%3d,", 0x80);
else printf("%3d,", 0);
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n\nnt16=>nt256char");
for (i=0; i<256; i++) {
if ((i & 0xF0) == 0x10) putchar('A');
else if ((i & 0xF0) == 0x20) putchar('C');
else if ((i & 0xF0) == 0x40) putchar('G');
else if ((i & 0xF0) == 0x80) putchar('T');
else if ((i & 0xF0) == 0xF0) putchar('N');
else putchar('=');
}
puts("\n");
puts("\n\nnt16 => nt256int");
for (i=0; i<256; i++) {
if ((i & 0xF0) == 0x10) printf("0,");
else if ((i & 0xF0) == 0x20) printf("1,");
else if ((i & 0xF0) == 0x40) printf("2,");
else if ((i & 0xF0) == 0x80) printf("3,");
else printf("4,");
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n\nnt16 rev");
for (i=0; i<256; i++) {
j=i;
j=((j & 0xF0)>>4 | (j & 0x0F)<<4);
j=((j & 0xCC)>>2 | (j & 0x33)<<2);
j=((j & 0xAA)>>1 | (j & 0x55)<<1);
printf("%3d,", j);
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n\nnt256car => nt8");
for (i=0; i<256; i++) {
if (i == 'A') printf("%3d,", 0x00);
else if (i == 'C') printf("%3d,", 0x20);
else if (i == 'G') printf("%3d,", 0xC0);
else if (i == 'T') printf("%3d,", 0xE0);
else printf("%3d,", 0xA0);
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n\nnt8=>nt256char");
for (i=0; i<256; i++) {
if ((i & 0xE0) == 0x00) putchar('A');
else if ((i & 0xE0) == 0x20) putchar('C');
else if ((i & 0xE0) == 0xC0) putchar('G');
else if ((i & 0xE0) == 0xE0) putchar('T');
else putchar('N');
}
puts("\n");
puts("\n\nnt8 rev");
for (i=0; i<256; i++) {
if ((i & 0xE0) == 0x00) printf("%3d,", 0xE0);
else if ((i & 0xE0) == 0x20) printf("%3d,", 0xC0);
else if ((i & 0xE0) == 0xC0) printf("%3d,", 0x20);
else if ((i & 0xE0) == 0xE0) printf("%3d,", 0x00);
else printf("%3d,", (~i & 0xE0));
if (((i+1) & 0xf) == 0) printf("\n");
}
puts("\n");
puts("\n\nnt256char rev");
for (i=0; i<128; i++) {
if (i=='A') putchar('T');
else if (i=='T') putchar('A');
else if (i=='C') putchar('G');
else if (i=='G') putchar('C');
else putchar('N');
}
puts("\n");
return 0;
}
#endif
#ifdef MAIN_ENCODE
int main() {
char *seq_nt256char = "AAAAGGAACTTAGTGAAATTTTAGGTAGAAAGTTGACAGGGTACCAGGAGATGATGTAAGGGACAAGCAGCCACACCCCATTCTTGAGGGGCTGAGGTGGAAGAGACAGGCCCGGAGGGGTGAGGCAGTCTTTACTCACCTGTAGATGTCTCGGGCCATCCCGAAGTCTCCAATCTTGGCCACTCTTCCAGGGCCTGGACAGGTCAAGAGGCAGTTTCTGGCAGCAATGTCTCTGGGAAGAAAGGAAATGCATTTCCTAATTTTATCCCTAGGAAGATGAGTGTACAACGGCCATCACTAG";
/* char *seq_nt256char = "ATGCATGCAAG"; */
size_t l = strlen(seq_nt256char);
printf("seq_nt256char: %s\n", seq_nt256char);
puts("\n\n==== test nt4 ====");
uint8_t *seq_nt4 = cstr_encode_nt4(seq_nt256char);
puts("encode to nt4:");
bitarr_show(seq_nt4, LEN_NT256_TO_NT4(l));
printf("seq_nt256char (decoded): %s\n", nt4_decode_cstr(seq_nt4, l));
printf("seq_nt256char rev: %s\n", nt4_decode_cstr(nt4_rev(seq_nt4, l), l));
nt4_rev_ip(seq_nt4, l);
printf("seq_nt256char rev in-place: %s\n", nt4_decode_nt256char(seq_nt4, l));
printf("transcode to nt16:\n");
uint8_t *seq_nt16tr=nt4_decode_nt16(seq_nt4, l);
bitarr_show(seq_nt16tr, LEN_NT256_TO_NT16(l));
printf("decoded %s\n", nt16_decode_cstr(seq_nt16tr, l));
puts("\n\n==== test nt16 =====");
uint8_t *seq_nt16 = cstr_encode_nt16(seq_nt256char);
puts("encode to nt16:");
bitarr_show(seq_nt16, LEN_NT256_TO_NT16(l));
printf("seq_nt256char (decoded): %s\n", nt16_decode_cstr(seq_nt16, l));
puts("reverse nt16:");
bitarr_show(nt16_rev(seq_nt16, l), LEN_NT256_TO_NT16(l));
printf("reversed decoded: %s\n", nt16_decode_cstr(nt16_rev(seq_nt16, l), l));
puts("\n\n===== test nt256int8 ====");
int8_t *seq_nt256int8 = cstr_encode_nt256int8(seq_nt256char);
puts("encode to nt256int8 and decode back:");
puts(nt256int8_decode_cstr(seq_nt256int8, l));
puts("reversed");
puts(nt256int8_decode_cstr(nt256int8_rev(seq_nt256int8, l), l));
puts("transcode from nt16:");
puts(nt16_decode_cstr(seq_nt16, l));
seq_nt256int8 = nt16_decode_nt256int8(seq_nt16,l);
puts(nt256int8_decode_nt256char(seq_nt256int8, l));
puts("\n\n===== test nt8 ====");
int8_t *seq_nt8 = cstr_encode_nt8(seq_nt256char);
bitarr_show(seq_nt8, LEN_NT256_TO_NT8(l));
printf("decoded: %s\n", nt8_decode_cstr(seq_nt8, l));
printf("reversed: %s\n", nt8_decode_cstr(nt8_rev(seq_nt8, l), l));
return 0;
}
#endif