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dna.h
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dna.h
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/*
*
* Copyright (c) 2011, Jue Ruan <ruanjue@gmail.com>
*
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __DNA_RJ_H
#define __DNA_RJ_H
#include <stdint.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include "list.h"
#include "bitvec.h"
#include "hashset.h"
#include "thread.h"
static const u1i base_bit_table[256] = {
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, 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, 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, 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
};
static const u1i base_bit4_table[256] = {
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 1, 14, 2, 13, 15, 15, 4, 11, 15, 15, 12, 15, 3, 15, 15,
15, 15, 5, 6, 8, 15, 7, 9, 15, 10, 15, 15, 15, 15, 15, 15,
15, 1, 14, 2, 13, 15, 15, 4, 11, 15, 15, 12, 15, 3, 15, 15,
15, 15, 5, 6, 8, 15, 7, 9, 15, 10, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15
};
static const u1i bit4_bit_table[16] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 };
static const char bit_base_table[12] = "ACGTN-acgtn*";
static const char bit4_base_table[16] = "-ACMGRSVTWYHKDBN";
// u8i = 0|1|2|3|4|5|6|...
#define bits2bit(bits, off) (((bits)[(off) >> 5] >> (((~(off)) & 0x1FU) << 1)) & 0x03U)
#define bits2revbit(bits, off) ((~((bits)[(off) >> 5] >> (((~(off)) & 0x1FU) << 1))) & 0x03U)
static inline u8i dna_xor2ones(u8i seq){
return ((seq & 0xAAAAAAAAAAAAAAAALLU) >> 1) | (seq & 0x5555555555555555LLU);
}
static inline u8i dna_rev_seq32(u8i seq){
seq = ~seq;
seq = ((seq & 0x3333333333333333LLU)<< 2) | ((seq & 0xCCCCCCCCCCCCCCCCLLU)>> 2);
seq = ((seq & 0x0F0F0F0F0F0F0F0FLLU)<< 4) | ((seq & 0xF0F0F0F0F0F0F0F0LLU)>> 4);
#if 0
seq = ((seq & 0x00FF00FF00FF00FFLLU)<< 8) | ((seq & 0xFF00FF00FF00FF00LLU)>> 8);
seq = ((seq & 0x0000FFFF0000FFFFLLU)<<16) | ((seq & 0xFFFF0000FFFF0000LLU)>>16);
seq = ((seq & 0x00000000FFFFFFFFLLU)<<32) | ((seq & 0xFFFFFFFF00000000LLU)>>32);
#else
seq = __builtin_bswap64(seq);
#endif
return seq;
}
static inline u8i dna_rev_seq(u8i seq, u1i seq_size){
return dna_rev_seq32(seq) >> (64 - (seq_size<<1));
}
// order of 2-bit in this->seqs is different with that in dna_rev_seq->seq
static inline void dna_rev_seqs(u8i *seqs, u8i seq_size){
register u8i t;
int i, j;
register u1i d, e;
j = (seq_size + 31) >> 5;
// Swap within 64bit
for(i=0;i<j;i++){
seqs[i] = ~seqs[i];
seqs[i] = ((seqs[i] & 0x3333333333333333LLU)<< 2) | ((seqs[i] & 0xCCCCCCCCCCCCCCCCLLU)>> 2);
seqs[i] = ((seqs[i] & 0x0F0F0F0F0F0F0F0FLLU)<< 4) | ((seqs[i] & 0xF0F0F0F0F0F0F0F0LLU)>> 4);
seqs[i] = __builtin_bswap64(seqs[i]);
}
// Swap 64bit blocks
for(i=0;i<j>>1;i++){
t = seqs[i]; seqs[i] = seqs[j - i - 1]; seqs[j - i - 1] = t;
}
// left-align seqs
if((d = ((j << 5) - seq_size) << 1)){
e = 64 - d;
for(i=0;i<j-1;i++){
seqs[i] = (seqs[i] << d) | (seqs[i+1] >> e);
}
seqs[i] = (seqs[i] << d) | 0;
}
}
//shift one base, and append one base, useful to build big-kmer
static inline void dna_shl_seqs(u8i *seqs, u8i seq_size, u1i base_val){
const u1i d = 2;
const u1i e = 62;
int i, j;
j = (seq_size + 31) >> 5;
for(i=0;i<j-1;i++){
seqs[i] = (seqs[i] << d) | (seqs[i+1] >> e);
}
seqs[i] = (seqs[i] << d) | (((u8i)(base_val & 0x03U)) << ((32 - (seq_size & 0x1FU)) << 1));
}
static inline int dna_cmp_seqs(u8i *seqs1, u8i *seqs2, u8i seq_size){
int i, j;
j = (seq_size + 31) >> 5;
for(i=0;i<j;i++){
if(seqs1[i] < seqs2[i]) return -1;
if(seqs1[i] > seqs2[i]) return 1;
}
return 0;
}
static inline int dna_cmpx_seqs(u8i *seqs, u8i seq_size){
register int i, j;
register u1i a, b;
j = (seq_size + 1) >> 1;
for(i=0;i<j;i++){
a = bits2bit(seqs, i);
b = (~bits2bit(seqs, seq_size - 1 - i)) & 0x03U;
if(a < b) return -1;
if(a > b) return 1;
}
return 0;
}
static inline u8i seq2kmer(char *seq, u4i ksize){
u8i kmer;
u4i i;
kmer = 0;
for(i=0;i<ksize;i++) kmer = (kmer << 2) | base_bit_table[(int)seq[i]];
return kmer;
}
static inline u8i seq2revkmer(char *seq, u4i ksize){
u8i kmer;
u4i i;
kmer = 0;
for(i=0;i<ksize;i++) kmer = (kmer << 2) | ((~base_bit_table[(int)seq[ksize - 1 - i]]) & 0x03);
return kmer;
}
static inline void kmer2seq(char *seq, u8i kmer, u4i ksize){
u4i i;
for(i=0;i<ksize;i++){
seq[i] = bit_base_table[(kmer >> ((ksize - 1 - i) << 1)) & 0x03];
}
seq[i] = 0;
}
static inline void kmer2revseq(char *seq, u8i kmer, u4i ksize){
u4i i;
kmer = ~kmer;
for(i=0;i<ksize;i++){
seq[i] = bit_base_table[(kmer >> (i << 1)) & 0x03];
}
seq[i] = 0;
}
static inline void print_kmer_seq(u8i kmer, u4i ksize, FILE *out){
char seq[33];
kmer2seq(seq, kmer, ksize);
fputs(seq, out);
}
static inline void print_kmer_revseq(u8i kmer, u4i ksize, FILE *out){
char seq[33];
kmer2revseq(seq, kmer, ksize);
fputs(seq, out);
}
#define kmer_mask(ksize) (0xFFFFFFFFFFFFFFFFLLU >> ((32 - (ksize)) * 2))
#define beg_seq2kmers(seq, seqlen, ksize, kmask, kmer, idx) { \
u1i beg_seq2kmers_v; \
kmer = 0; \
for(idx=0;(int)idx+1<(int)ksize;idx++){ \
beg_seq2kmers_v = base_bit_table[(int)(seq)[idx]]; \
if(beg_seq2kmers_v == 4) beg_seq2kmers_v = lrand48() & 0x03; \
kmer = (((kmer) << 2) | beg_seq2kmers_v); \
} \
for(idx=0;(int)idx<=(int)(seqlen-ksize);idx++){ \
beg_seq2kmers_v = base_bit_table[(int)(seq)[idx + (ksize) - 1]]; \
if(beg_seq2kmers_v == 4) beg_seq2kmers_v = lrand48() & 0x03; \
kmer = ((kmer << 2) | beg_seq2kmers_v) & kmask;
#define end_seq2kmers } }
#define beg_seq2revkmers(seq, seqlen, ksize, kmask, kmer, idx) { \
u1i beg_seq2revkmers_v; \
kmer = 0; \
for(idx=0;(int)idx+1<(int)ksize;idx++){ \
beg_seq2revkmers_v = base_bit_table[(int)(seq)[seqlen - 1 - idx]]; \
if(beg_seq2revkmers_v == 4) beg_seq2revkmers_v = lrand48() & 0x03; \
kmer = (((kmer) << 2) | beg_seq2revkmers_v); \
} \
for(idx=0;(int)idx<=(int)seqlen-ksize;idx++){ \
beg_seq2revkmers_v = base_bit_table[(int)(seq)[seqlen - idx - (ksize)]]; \
if(beg_seq2revkmers_v == 4) beg_seq2revkmers_v = lrand48() & 0x03; \
kmer = ((kmer << 2) | beg_seq2revkmers_v) & kmask;
#define end_seq2revkmers } }
static inline char reverse_dna_base(char b){
switch(b){
case 'a': return 't';
case 'A': return 'T';
case 'c': return 'g';
case 'C': return 'G';
case 'g': return 'c';
case 'G': return 'C';
case 't': return 'a';
case 'T': return 'A';
default: return 'N';
}
}
static inline void reverse_dna(char *seq, int len){
int i, j;
char c;
i = 0;
j = len - 1;
while(i < j){
c = seq[i]; seq[i] = seq[j]; seq[j] = c;
i ++; j --;
}
for(i=0;i<len;i++){
switch(seq[i]){
case 'a': seq[i] = 't'; break;
case 'A': seq[i] = 'T'; break;
case 'c': seq[i] = 'g'; break;
case 'C': seq[i] = 'G'; break;
case 'g': seq[i] = 'c'; break;
case 'G': seq[i] = 'C'; break;
case 't': seq[i] = 'a'; break;
case 'T': seq[i] = 'A'; break;
}
}
}
#define reverse_dna_coord(x, y, tot_len) { x = x ^ y; y = x ^ y; x = x ^ y; x = tot_len - x; y = tot_len - y; }
#define old_bit2bits(bits, off, bit) { if(((off) & 0x1FU) == 0) (bits)[(off) >> 5] = 0; (bits)[(off) >> 5] |= ((u8i)(bit)) << (((~(off)) & 0x1FU) << 1); }
#define bit2bits(bits, off, bit) { \
u8i __off1; \
u4i __off2; \
__off1 = (off) >> 5; \
__off2 = (((~(off)) & 0x1FU) << 1); \
(bits)[__off1] = ((bits)[__off1] & (~(0x3LLU << __off2))) | (((u8i)(bit)) << __off2); \
}
static inline void seq2bits(u8i *bits, u8i bitoff, char *seq, u4i seqlen){
u8i i, c;
for(i=0;i<seqlen;i++){
c = base_bit_table[(int)seq[i]];
if(c == 4) c = lrand48() & 0x03;
bit2bits(bits, bitoff + i, c);
}
}
static inline void revseq2bits(u8i *bits, u8i bitoff, char *seq, u4i seqlen){
u8i i, c;
for(i=0;i<seqlen;i++){
c = base_bit_table[(int)seq[seqlen - i - 1]];
if(c == 4) c = lrand48();
c = (~c) & 0x03;
bit2bits(bits, bitoff + i, c);
}
}
static inline void bits2seq(char *seq, u8i *bits, u8i off, u4i len){
u4i i, c;
for(i=0;i<len;i++){
c = bits2bit(bits, off + i);
seq[i] = bit_base_table[c];
}
seq[i] = 0;
}
static inline void bits2revseq(char *seq, u8i *bits, u8i off, u4i len){
u4i i, c;
for(i=0;i<len;i++){
c = (bits[(off + i)>>5] >> (((~(off + i)) & 0x1FU) << 1)) & 0x03;
seq[len - i - 1] = bit_base_table[(~c)&0x03];
}
seq[i] = 0;
}
static inline u8i sub32seqbits(u8i *src, u8i off){
u8i m;
u4i n;
m = off >> 5;
n = (off & 0x1F) << 1;
return (src[m] << n) | (((src[m + 1] >> (62 - n)) >> 2));
//n = off & 0x1F;
//if(n){
//return (src[m] << (n << 1)) | (src[m + 1] >> ((32 - n) << 1));
//} else {
//return src[m];
//}
}
static inline u8i sub8seqbits(u8i *src, u8i off){
u8i off1;
u4i off2;
off1 = off >> 5;
off2 = (off & 0x1FU) << 1;
return ((src[off1] << off2) | (((src[off1 + 1] >> (62 - off2)) >> 2))) >> 48;
}
static inline u8i sub4seqbits(u8i *src, u8i off){
u8i off1;
u4i off2;
off1 = off >> 5;
off2 = (off & 0x1FU) << 1;
return ((src[off1] << off2) | (((src[off1 + 1] >> (62 - off2)) >> 2))) >> 56;
}
static inline u8i sub2seqbits(u8i *src, u8i off){
u8i off1;
u4i off2;
off1 = off >> 5;
off2 = (off & 0x1FU) << 1;
return ((src[off1] << off2) | (((src[off1 + 1] >> (62 - off2)) >> 2))) >> 60;
}
static inline u8i sub_seqbits(u8i *src, u8i off, u1i len){
u8i off1;
u4i off2;
off1 = off >> 5;
off2 = (off & 0x1FU) << 1;
return ((src[off1] << off2) | (((src[off1 + 1] >> (62 - off2)) >> 2))) >> ((32 - len) << 1);
}
#define subseqbits(src, off, len) sub_seqbits(src, off, len)
static inline int cmpgt_seqbits(u8i *bits, u8i off1, u8i off2, u4i _len){
u8i idxs[2], v[2];
u4i offs[2], i, len;
idxs[0] = off1 >> 5;
idxs[1] = off2 >> 5;
offs[0] = (off1 & 0x1FU) << 1;
offs[1] = (off2 & 0x1FU) << 1;
len = roundup_times(_len, 32);
for(i=0;i<len;i+=32){
v[0] = (bits[idxs[0]] << offs[0]) | (((bits[idxs[0] + 1] >> (62 - offs[0])) >> 2));
v[1] = (bits[idxs[1]] << offs[1]) | (((bits[idxs[1] + 1] >> (62 - offs[1])) >> 2));
if(v[0] > v[1]){
return 1;
} else if(v[0] < v[1]){
return 0;
}
idxs[0] ++;
idxs[1] ++;
}
return 0;
}
#if __BYTE_ORDER == 1234
static const u4i spare_2bits_table[256] = {
0, 16777216, 33554432, 50331648, 65536, 16842752, 33619968, 50397184,
131072, 16908288, 33685504, 50462720, 196608, 16973824, 33751040, 50528256,
256, 16777472, 33554688, 50331904, 65792, 16843008, 33620224, 50397440,
131328, 16908544, 33685760, 50462976, 196864, 16974080, 33751296, 50528512,
512, 16777728, 33554944, 50332160, 66048, 16843264, 33620480, 50397696,
131584, 16908800, 33686016, 50463232, 197120, 16974336, 33751552, 50528768,
768, 16777984, 33555200, 50332416, 66304, 16843520, 33620736, 50397952,
131840, 16909056, 33686272, 50463488, 197376, 16974592, 33751808, 50529024,
1, 16777217, 33554433, 50331649, 65537, 16842753, 33619969, 50397185,
131073, 16908289, 33685505, 50462721, 196609, 16973825, 33751041, 50528257,
257, 16777473, 33554689, 50331905, 65793, 16843009, 33620225, 50397441,
131329, 16908545, 33685761, 50462977, 196865, 16974081, 33751297, 50528513,
513, 16777729, 33554945, 50332161, 66049, 16843265, 33620481, 50397697,
131585, 16908801, 33686017, 50463233, 197121, 16974337, 33751553, 50528769,
769, 16777985, 33555201, 50332417, 66305, 16843521, 33620737, 50397953,
131841, 16909057, 33686273, 50463489, 197377, 16974593, 33751809, 50529025,
2, 16777218, 33554434, 50331650, 65538, 16842754, 33619970, 50397186,
131074, 16908290, 33685506, 50462722, 196610, 16973826, 33751042, 50528258,
258, 16777474, 33554690, 50331906, 65794, 16843010, 33620226, 50397442,
131330, 16908546, 33685762, 50462978, 196866, 16974082, 33751298, 50528514,
514, 16777730, 33554946, 50332162, 66050, 16843266, 33620482, 50397698,
131586, 16908802, 33686018, 50463234, 197122, 16974338, 33751554, 50528770,
770, 16777986, 33555202, 50332418, 66306, 16843522, 33620738, 50397954,
131842, 16909058, 33686274, 50463490, 197378, 16974594, 33751810, 50529026,
3, 16777219, 33554435, 50331651, 65539, 16842755, 33619971, 50397187,
131075, 16908291, 33685507, 50462723, 196611, 16973827, 33751043, 50528259,
259, 16777475, 33554691, 50331907, 65795, 16843011, 33620227, 50397443,
131331, 16908547, 33685763, 50462979, 196867, 16974083, 33751299, 50528515,
515, 16777731, 33554947, 50332163, 66051, 16843267, 33620483, 50397699,
131587, 16908803, 33686019, 50463235, 197123, 16974339, 33751555, 50528771,
771, 16777987, 33555203, 50332419, 66307, 16843523, 33620739, 50397955,
131843, 16909059, 33686275, 50463491, 197379, 16974595, 33751811, 50529027
};
#else
static const u4i spare_2bits_table[256] = {
0, 1, 2, 3, 256, 257, 258, 259,
512, 513, 514, 515, 768, 769, 770, 771,
65536, 65537, 65538, 65539, 65792, 65793, 65794, 65795,
66048, 66049, 66050, 66051, 66304, 66305, 66306, 66307,
131072, 131073, 131074, 131075, 131328, 131329, 131330, 131331,
131584, 131585, 131586, 131587, 131840, 131841, 131842, 131843,
196608, 196609, 196610, 196611, 196864, 196865, 196866, 196867,
197120, 197121, 197122, 197123, 197376, 197377, 197378, 197379,
16777216, 16777217, 16777218, 16777219, 16777472, 16777473, 16777474, 16777475,
16777728, 16777729, 16777730, 16777731, 16777984, 16777985, 16777986, 16777987,
16842752, 16842753, 16842754, 16842755, 16843008, 16843009, 16843010, 16843011,
16843264, 16843265, 16843266, 16843267, 16843520, 16843521, 16843522, 16843523,
16908288, 16908289, 16908290, 16908291, 16908544, 16908545, 16908546, 16908547,
16908800, 16908801, 16908802, 16908803, 16909056, 16909057, 16909058, 16909059,
16973824, 16973825, 16973826, 16973827, 16974080, 16974081, 16974082, 16974083,
16974336, 16974337, 16974338, 16974339, 16974592, 16974593, 16974594, 16974595,
33554432, 33554433, 33554434, 33554435, 33554688, 33554689, 33554690, 33554691,
33554944, 33554945, 33554946, 33554947, 33555200, 33555201, 33555202, 33555203,
33619968, 33619969, 33619970, 33619971, 33620224, 33620225, 33620226, 33620227,
33620480, 33620481, 33620482, 33620483, 33620736, 33620737, 33620738, 33620739,
33685504, 33685505, 33685506, 33685507, 33685760, 33685761, 33685762, 33685763,
33686016, 33686017, 33686018, 33686019, 33686272, 33686273, 33686274, 33686275,
33751040, 33751041, 33751042, 33751043, 33751296, 33751297, 33751298, 33751299,
33751552, 33751553, 33751554, 33751555, 33751808, 33751809, 33751810, 33751811,
50331648, 50331649, 50331650, 50331651, 50331904, 50331905, 50331906, 50331907,
50332160, 50332161, 50332162, 50332163, 50332416, 50332417, 50332418, 50332419,
50397184, 50397185, 50397186, 50397187, 50397440, 50397441, 50397442, 50397443,
50397696, 50397697, 50397698, 50397699, 50397952, 50397953, 50397954, 50397955,
50462720, 50462721, 50462722, 50462723, 50462976, 50462977, 50462978, 50462979,
50463232, 50463233, 50463234, 50463235, 50463488, 50463489, 50463490, 50463491,
50528256, 50528257, 50528258, 50528259, 50528512, 50528513, 50528514, 50528515,
50528768, 50528769, 50528770, 50528771, 50529024, 50529025, 50529026, 50529027
};
#endif
static inline void spare_2bits(u1i bs[32], u8i v){
((u4i*)bs)[0] = spare_2bits_table[((v >> 56) & 0xFF)];
((u4i*)bs)[1] = spare_2bits_table[((v >> 48) & 0xFF)];
((u4i*)bs)[2] = spare_2bits_table[((v >> 40) & 0xFF)];
((u4i*)bs)[3] = spare_2bits_table[((v >> 32) & 0xFF)];
((u4i*)bs)[4] = spare_2bits_table[((v >> 24) & 0xFF)];
((u4i*)bs)[5] = spare_2bits_table[((v >> 16) & 0xFF)];
((u4i*)bs)[6] = spare_2bits_table[((v >> 8) & 0xFF)];
((u4i*)bs)[7] = spare_2bits_table[((v >> 0) & 0xFF)];
}
typedef struct {
u8i *bits;
u8i size;
u8i cap;
} BaseBank;
static inline size_t basebank_obj_desc_cnt(void *obj, int idx){ return ((((BaseBank*)obj)->size + 31) / 32 + 1) * 8; idx = idx; }
static inline void basebank_obj_desc_post_load(void *obj, size_t aux_data){
BaseBank *bnk;
UNUSED(aux_data);
bnk = (BaseBank*)obj;
bnk->cap = ((bnk->size + 31) / 32) * 32;
}
static const obj_desc_t basebank_obj_desc = {"BaseBank", sizeof(BaseBank), 1, {1}, {offsetof(BaseBank, bits)}, {(obj_desc_t*)&OBJ_DESC_DATA}, basebank_obj_desc_cnt, basebank_obj_desc_post_load};
static inline BaseBank* init_basebank(){
BaseBank *bnk;
bnk = malloc(sizeof(BaseBank));
bnk->size = 0;
bnk->cap = 256;
bnk->bits = calloc(bnk->cap / 32 + 1, 8);
return bnk;
}
static inline void free_basebank(BaseBank *bnk){
free(bnk->bits);
free(bnk);
}
static inline void encap_basebank(BaseBank *bnk, u8i inc){
u8i old;
u8i *bits;
if(bnk->cap - bnk->size >= inc) return;
old = bnk->cap;
if(MAX_U8 - inc <= bnk->size){
fprintf(stderr, " -- Overflow(64bits) %llu + %llu, in %s -- %s:%d --\n", (u8i)bnk->size, (u8i)inc, __FUNCTION__, __FILE__, __LINE__);
print_backtrace(stderr, 20);
abort();
}
if(MAX_U8 - inc < 0x3FFFFFFFLLU){
fprintf(stderr, " -- Overflow(64bits) %llu + %llu, in %s -- %s:%d --\n", (u8i)bnk->size, (u8i)inc, __FUNCTION__, __FILE__, __LINE__);
print_backtrace(stderr, 20);
abort();
}
if(bnk->size + inc <= 0x3FFFFFFFLLU){
bnk->cap = roundup_times(2 * (bnk->size + inc), 32);
} else {
//bnk->cap = ((bnk->size + inc + 0xFFFFFFFLLU - 1LLU) / 0xFFFFFFFLLU) * 0xFFFFFFFLLU;
bnk->cap = (bnk->size + inc + 0x3FFFFFFFLLU) & (MAX_U8 << 30);
}
if(bnk->cap < 32) bnk->cap = 32;
bits = realloc(bnk->bits, ((bnk->cap >> 5) + 1) << 3);
if(bits == NULL){
fprintf(stderr, " -- Out of memory, try to allocate %llu bytes, old size %llu, in %s -- %s:%d --\n", (u8i)bnk->cap >> 2, old >> 2, __FUNCTION__, __FILE__, __LINE__);
print_backtrace(stderr, 20);
abort();
}
bnk->bits = bits;
memset(bnk->bits + (old / 32), 0, (bnk->cap + 32 - old) / 4);
}
static inline void clear_basebank(BaseBank *bnk){
//memset(bnk->bits, 0, ((bnk->size + 31) / 32) * 8);
bnk->size = 0;
}
static inline void normalize_basebank(BaseBank *bnk){
if(bnk->size < bnk->cap){
if(bnk->size & 0x1FU){
bnk->bits[bnk->size>>5] = bnk->bits[bnk->size>>5] & (MAX_U8 << (64 - ((bnk->size & 0x1FU) << 1)));
}
}
}
static inline void pack_basebank(BaseBank *bnk){
u8i size;
size = (bnk->size + 31) & (~0x1FLLU);
if(size == 0) size = 32;
if(size >= bnk->cap) return;
bnk->cap = ((size + 31) / 32) * 32;
bnk->bits = realloc(bnk->bits, ((bnk->cap >> 5) + 1) << 3);
memset(bnk->bits + (bnk->cap >> 5), 0, 8);
}
static inline void bit2basebank(BaseBank *bnk, u1i v){
encap_basebank(bnk, 1);
bit2bits(bnk->bits, bnk->size, (v & 0x03));
bnk->size ++;
}
static inline void bits2basebank(BaseBank *bnk, u8i *bits, u8i off, u8i len){
u8i offset;
encap_basebank(bnk, len);
for(offset=off;offset<off+len;offset++){
bit2bits(bnk->bits, bnk->size, bits2bit(bits, offset));
bnk->size ++;
}
}
#define fwdbits2basebank(bnk, bits, off, len) bits2basebank(bnk, bits, off, len)
static inline void fast_bits2basebank(BaseBank *bnk, u8i *bits, u8i off, u8i len){
u8i end, dat;
u4i gap;
encap_basebank(bnk, len);
if(len == 0) return;
if(bnk->size & 0x1FU){
gap = 32 - (bnk->size & 0x1FU);
if(len <= gap){
dat = subseqbits(bits, off, len);
bnk->bits[bnk->size >> 5] |= dat << ((gap - len) << 1);
bnk->size += len;
return;
} else {
dat = subseqbits(bits, off, gap);
bnk->bits[bnk->size >> 5] |= dat;
bnk->size += gap;
off += gap;
len -= gap;
}
}
end = off + len;
for(;off+32<=end;off+=32){
dat = sub32seqbits(bits, off);
bnk->bits[bnk->size >> 5] = dat;
bnk->size += 32;
}
if(off < end){
dat = sub32seqbits(bits, off);
bnk->bits[bnk->size >> 5] = dat & (MAX_U8 << ((32 - (end - off)) << 1));
bnk->size += end - off;
} else {
bnk->bits[bnk->size >> 5] = 0;
}
}
#define fast_fwdbits2basebank(bnk, bits, off, len) fast_bits2basebank(bnk, bits, off, len)
static inline void revbits2basebank(BaseBank *bnk, u8i *bits, u8i off, u8i len){
u8i i;
encap_basebank(bnk, len);
for(i=1;i<=len;i++){
bit2bits(bnk->bits, bnk->size, bits2revbit(bits, (off + len - i)));
bnk->size ++;
}
}
static inline void fast_revbits2basebank(BaseBank *bnk, u8i *bits, u8i off, u8i len){
u8i end, dat;
u4i gap;
if(len == 0) return;
encap_basebank(bnk, len);
if(bnk->size & 0x1FU){
gap = 32 - (bnk->size & 0x1FU);
if(len <= gap){
dat = subseqbits(bits, off, len);
dat = dna_rev_seq(dat, len);
bnk->bits[bnk->size >> 5] |= dat << ((gap - len) << 1);
bnk->size += len;
return;
} else {
dat = subseqbits(bits, off + len - gap, gap);
dat = dna_rev_seq(dat, gap);
bnk->bits[bnk->size >> 5] |= dat;
bnk->size += gap;
//off += gap;
len -= gap;
}
}
end = off + len;
for(;off+32<=end;){
end -= 32;
dat = sub32seqbits(bits, end);
dat = dna_rev_seq32(dat);
bnk->bits[bnk->size >> 5] = dat;
bnk->size += 32;
}
if(off < end){
dat = sub32seqbits(bits, off);
dat = dna_rev_seq32(dat);
//bnk->bits[bnk->size >> 5] = dat & (MAX_U8 << ((32 - (end - off)) << 1));
bnk->bits[bnk->size >> 5] = dat << ((32 - (end - off)) << 1);
bnk->size += end - off;
} else {
bnk->bits[bnk->size >> 5] = 0;
}
}
static inline void seq2basebank(BaseBank *bnk, char *seq, u8i len){
u8i idx1, i, c;
u1i idx2;
encap_basebank(bnk, len);
idx1 = bnk->size >> 5;
idx2 = ((bnk->size) & 0x1FU) << 1;
bnk->size += len;
if(idx2 == 0) bnk->bits[idx1] = 0;
for(i=0;i<len;i++){
c = base_bit_table[(int)seq[i]] & 0x03;
bnk->bits[idx1] |= c << (62 - idx2);
idx2 = (idx2 + 2) & 0x3F;
if(idx2 == 0){
bnk->bits[++idx1] = 0;
}
}
}
#define fwdseq2basebank(bnk, seq, len) seq2basebank(bnk, seq, len)
static inline void revseq2basebank(BaseBank *bnk, char *seq, u8i len){
char *p;
u1i c;
p = seq + len;
encap_basebank(bnk, len);
while(p > seq){
p --;
c = base_bit_table[(int)*p];
c = (~c) & 0x03;
bit2bits(bnk->bits, bnk->size, c);
bnk->size ++;
}
}
static inline void seq2basebank2(BaseBank *bnk, char *seq, u8i len){
char *p;
u1i c;
p = seq;
seq = seq + len;
encap_basebank(bnk, len);
while(p < seq){
c = base_bit_table[(int)*p];
if(c == 4) c = lrand48() & 0x03;
bit2bits(bnk->bits, bnk->size, c);
bnk->size ++;
p ++;
}
}
static inline void revseq2basebank2(BaseBank *bnk, char *seq, u8i len){
char *p;
u1i c;
p = seq + len;
encap_basebank(bnk, len);
while(p > seq){
p --;
c = base_bit_table[(int)*p];
if(c == 4) c = lrand48() & 0x03;
c = (~c) & 0x03;
bit2bits(bnk->bits, bnk->size, c);
bnk->size ++;
}
}
static inline u1i get_basebank(BaseBank *bnk, u8i off){ return bits2bit(bnk->bits, off); }
static inline void seq_basebank(BaseBank *bnk, u8i off, u8i len, char *seq){
u8i i;
for(i=0;i<len;i++){
seq[i] = bit_base_table[bits2bit(bnk->bits, off + i)];
}
seq[i] = 0;
}
#define fwdseq_basebank(bnk, off, len, seq) seq_basebank(bnk, off, len, seq)
static inline void bitseq_basebank(BaseBank *bnk, u8i off, u8i len, u1i *seq){
u8i i;
for(i=0;i<len;i++){
seq[i] = bits2bit(bnk->bits, off + i);
}
}
static inline void revseq_basebank(BaseBank *bnk, u8i off, u8i len, char *seq){
u8i i;
for(i=0;i<len;i++){
seq[i] = bit_base_table[(~bits2bit(bnk->bits, off + len - 1 - i)) & 0x03];
}
seq[i] = 0;
}
static inline void revbitseq_basebank(BaseBank *bnk, u8i off, u8i len, u1i *seq){
u8i i;
for(i=0;i<len;i++){
seq[i] = (~bits2bit(bnk->bits, off + len - 1 - i)) & 0x03;
}
}
static inline void reverse_basebank(BaseBank *bnk){
u8i size, rsize;
size = bnk->size;
rsize = (bnk->size + 31) & (~0x1FLLU);
encap_basebank(bnk, rsize + 32);
memcpy(bnk->bits + (rsize >> 5), bnk->bits + 0, (rsize >> 5) << 3);
bnk->size = 0;
fast_revbits2basebank(bnk, bnk->bits, rsize, size);
}
static inline void print_seq_basebank(BaseBank *bnk, u8i off, u8i len, FILE *out){
u8i i, b, e;
char buf[101];
for(b=off;b<off+len;){
e = num_min(b + 100, off + len);
for(i=b;i<e;i++){
buf[i - b] = bit_base_table[bits2bit(bnk->bits, i)];
}
buf[e - b] = '\0';
fputs(buf, out);
//fputc('\n', out);
b = e;
}
}
static inline void print_lines_basebank(BaseBank *bnk, u8i off, u8i len, FILE *out, int linewidth){
u8i i, b, e;
char *buf;
if(linewidth < 1) linewidth = 100;
buf = malloc(linewidth + 1);
for(b=off;b<off+len;){
e = num_min(b + linewidth, off + len);
for(i=b;i<e;i++){
buf[i - b] = bit_base_table[bits2bit(bnk->bits, i)];
}
buf[e - b] = '\0';
fputs(buf, out);
fputc('\n', out);
b = e;
}
free(buf);
}
#define print_fwdseq_basebank(bnk, off, len, out) print_seq_basebank(bnk, off, len, out)
static inline void println_seq_basebank(BaseBank *bnk, u8i off, u8i len, FILE *out){
print_seq_basebank(bnk, off, len, out);
fputc('\n', out);
}
#define println_fwdseq_basebank(bnk, off, len, out) println_seq_basebank(bnk, off, len, out)
static inline void print_revseq_basebank(BaseBank *bnk, u8i off, u8i len, FILE *out){
u8i i;
char buf[65];
buf[64] = '\0';
for(i=0;i<len;){
buf[i & 0x3F] = bit_base_table[bits2revbit(bnk->bits, off + len - 1 - i)];
i ++;
if((i & 0x3F) == 0){
fprintf(out, "%s", buf);
}
}
if(i & 0x3F){
buf[i & 0x3F] = '\0';
fprintf(out, "%s", buf);
}
}
static inline u8i sub32_basebank(BaseBank *bnk, u8i off){ return sub32seqbits(bnk->bits, off); }
static inline u8i sub4_basebank(BaseBank *bnk, u8i off){ return sub4seqbits(bnk->bits, off); }
// assert(len > 0 && len <= 32)
static inline u8i subbits_basebank(BaseBank *bnk, u8i off, u1i len){ return sub_seqbits(bnk->bits, off, len); }
static inline void println_revseq_basebank(BaseBank *bnk, u8i off, u8i len, FILE *out){
print_revseq_basebank(bnk, off, len, out);
fputc('\n', out);
}
static inline u8i hzsubbits_basebank(BaseBank *bnk, u8i off, u1i len){
u8i k;
u1i i, b, c;
k = 0;
b = 4;
for(i=0;i<len;off++){
c = bits2bit(bnk->bits, off);
if(c == b) continue;
i ++;
b = c;
k = (k << 2) | b;
}
return k;
}
static inline int bitsearch_basebank(BaseBank *bnk, u8i *_off, u8i len, u8i bits, u1i size, int max_occ){
u8i off, end, k, mask;
u1i b;
int ret;
off = *_off;
end = off + len;
mask = MAX_U8 >> ((32 - size) << 1);
k = subbits_basebank(bnk, off, size - 1);
off += size - 1;
ret = 0;
for(;off<end;off++){
b = bits2bit(bnk->bits, off);
k = ((k << 2) | b) & mask;
if(k == bits){
_off[ret++] = off - (size - 1);
if(ret >= max_occ) break;
}
}
return ret;
}
static inline int hzbitsearch_basebank(BaseBank *bnk, u8i *_off, u8i len, u8i bits, u1i size, int max_occ){
u8i off, h, end, k, mask;
u1i b, c;
int ret;
off = *_off;
end = off + len;
mask = MAX_U8 >> ((32 - size) << 1);
k = 0;
h = 0;
b = 4;
ret = 0;
for(;off<end;off++){
c = bits2bit(bnk->bits, off);
if(c == b) continue;
b = c;
h ++;
k = ((k << 2) | b) & mask;
if(h >= size && k == bits){
_off[ret++] = off - (size - 1);
if(ret >= max_occ) break;
}
}
return ret;
}
static inline u4i mismatch_basebank(BaseBank *bnk, u8i off1, u8i off2, u4i len){
u8i seq1, seq2;
u4i mm, i;
mm = 0;
for(i=0;i+32<=len;i+=32){
seq1 = sub32seqbits(bnk->bits, off1 + i);
seq2 = sub32seqbits(bnk->bits, off2 + i);
mm += count_ones_bit64(dna_xor2ones(seq1 ^ seq2));
}
if(i < len){
seq1 = sub32seqbits(bnk->bits, off1 + i);
seq2 = sub32seqbits(bnk->bits, off2 + i);
mm += count_ones_bit64((dna_xor2ones(seq1 ^ seq2)) >> ((32 - (len - i)) << 1));
}
return mm;
}
thread_beg_def(_mradix);
BaseBank *bb;
u4i *counts[2];
u4i *offs;
u1v *lcps;
u4i size, klen;
int task;
FILE *log;
thread_end_def(_mradix);
thread_beg_func(_mradix);
BaseBank *bb;
u4i *offs, *counts[2];
u4i i, j, size, klen, m, n, v, t;
u4i ncpu, tidx;
bb = _mradix->bb;
counts[0] = calloc((MAX_U2 + 1), sizeof(u4i)); // used in twice
counts[1] = calloc((MAX_U2 + 1), sizeof(u4i));
ncpu = _mradix->n_cpu;
tidx = _mradix->t_idx;
thread_beg_loop(_mradix);
if(_mradix->task == 1){
size = _mradix->size;
for(i=_mradix->t_idx;i<size;i+=_mradix->n_cpu){
v = sub8seqbits(bb->bits, i);
counts[1][v] ++;
}
_mradix->counts[0] = counts[0];
_mradix->counts[1] = counts[1];
} else if(_mradix->task == 11){
offs = _mradix->offs;
size = _mradix->size;
for(i=0;i<size;i++){
v = sub8seqbits(bb->bits, i);
if((v % _mradix->n_cpu) == (u4i)_mradix->t_idx){
offs[_mradix->counts[0][v]++] = i;
}
if(_mradix->t_idx == 0 && _mradix->log && (i % 1000000) == 0){
fprintf(_mradix->log, "\r%u", i); fflush(_mradix->log);
}
}
if(_mradix->t_idx == 0 && _mradix->log){
fprintf(_mradix->log, "\r%u\n", size);
}
} else if(_mradix->task == 2) {
offs = _mradix->offs;
size = _mradix->size;
klen = _mradix->klen - 8;
if(size <= MAX_U1){
sort_array(offs, size, u4i, cmpgt_seqbits(bb->bits, a + 8, b + 8, klen)); // 8 bp already sorted
} else {
memset(counts[1], 0, (MAX_U1 + 1) * sizeof(u4i));
for(i=0;i<size;i++){
v = sub4seqbits(bb->bits, offs[i] + 8);
counts[1][v] ++;
}
m = 0;
for(i=0;i<=MAX_U1;i++){
counts[0][i] = m;
m += counts[1][i];
counts[1][i] = m;
}
for(m=0;m<=MAX_U1;m++){
while(counts[0][m] < counts[1][m]){
v = offs[counts[0][m]];
n = sub4seqbits(bb->bits, v + 8);
while(n > m){
t = offs[counts[0][n]];
offs[counts[0][n]] = v;
counts[0][n] ++;
v = t;