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kbm.h
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kbm.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 __KMER_BINMAP_RJ_H
#define __KMER_BINMAP_RJ_H
#include "list.h"
#include "hashset.h"
#include "dna.h"
#include "filereader.h"
#include "bitvec.h"
#include "bitsvec.h"
#include "bit2vec.h"
#include "thread.h"
#include "txtplot.h"
//#define __DEBUG__ 1
#define TEST_MODE
#define KBM_BIN_BITS 8
#define KBM_BSIZE 256
#define KBM_BIN_SIZE KBM_BSIZE
#define KBM_MAX_BINCNT 0xFFFFFFFFFFLLU // 40 bits, 1024 G
#define KBM_MAX_RDCNT 0x3FFFFFFF // 30 bits, 1 G
#define KBM_MAX_RDBINCNT 0x7FFFFF // 23 bits
// able to index reference sequences
#define KBM_MAX_RDLEN 0x7FFFFFFFU // 31 bits, 2 G bp
#define KBM_MAX_KSIZE 23
#define KBM_MAX_KCNT 0xFFFF // 16 bits, 65535
#define KBM_N_HASH 4096
#define KBM_LOGF stderr
#define KBM_LOGFNO STDERR_FILENO
static int KBM_LOG = 0;
#define KBM_LOG_LOW 1
#define KBM_LOG_MID 2
#define KBM_LOG_HIG 3
#define KBM_LOG_ALL 4
#define KBM_MAX_RDGRP1 0x7FFFFF
#define KBM_MAX_RDGRP2 0xFF
typedef struct {
u8i seqoff:40, flag:24; // seqoff is counted in BIN(256bp)
u8i binoff:40, bincnt:23, closed:1;
char *tag;
} kbm_read_t;
define_list(kbmreadv, kbm_read_t);
const obj_desc_t kbm_read_t_obj_desc = {"kbm_read_t_obj_desc", sizeof(kbm_read_t), 1, {1}, {offsetof(kbm_read_t, tag)}, {&OBJ_DESC_CHAR_ARRAY}, NULL, NULL};
static inline size_t kbmreadv_deep_obj_desc_cnt(void *list, int idx){ if(idx == 0) return ((kbmreadv*)list)->size; else return 0; }
static const obj_desc_t kbmreadv_deep_obj_desc = {.tag = "kbmreadv_deep_obj_desc", .size = sizeof(kbmreadv), .n_child = 1, .mem_type = {1}, .addr = {offsetof(kbmreadv, buffer)}, .desc = {&kbm_read_t_obj_desc}, .cnt = kbmreadv_deep_obj_desc_cnt, .post = NULL};
#define kbm_read_seqoff(rd) ((rd)->seqoff << KBM_BIN_BITS)
#define kbm_read_seqlen(rd) ((rd)->bincnt << KBM_BIN_BITS)
#define KBM_MAX_BIN_DEGREE 0x1FFU
// each BIN takes KBM_BIN_SIZE bp in uncompressed reads
typedef struct {
u4i ridx:30, off:24, closed:1, degree:9; // off * KBM_BIN_SIZE is the real position
} kbm_bin_t;
define_list(kbmbinv, kbm_bin_t);
typedef struct {
u4i bidx;
} kbm_bmer_t;
define_list(kbmbmerv, kbm_bmer_t);
typedef struct {
u1i bidx; // bidx = (kbm_baux_t->bidx << 32 | kbm_bmer_t->bidx)
u1i dir:1, koff:7; // koff is the real (offset? >> 1), here offset is +0 or +1
} kbm_baux_t;
define_list(kbmbauxv, kbm_baux_t);
#define getval_bidx(kbm, offset) ((((u8i)((kbm)->sauxs->buffer[offset].bidx)) << 32) | (kbm)->seeds->buffer[offset].bidx)
//#define kbm_kmer_smear(K) ((K) ^ ((K) >> 4) ^ ((K) >> 7) ^ ((K) >> 12))
#define kbm_kmer_smear(K) ((K) ^ ((K) >> 4) ^ ((K) >> 7))
typedef struct {
u8i mer:46, tot:17, flt:1;
} kbm_kmer_t;
define_list(kbmkmerv, kbm_kmer_t);
#define KBM_KMERCODE(E) ((E).mer)
#define KBM_KMEREQUALS(E1, E2) ((E1).mer == (E2).mer)
#define KBM_KEYEQUALS(K, E) ((K) == (E).mer)
define_hashtable(kbmhash, kbm_kmer_t, KBM_KMERCODE, KBM_KMEREQUALS, u8i, ITSELF, KBM_KEYEQUALS, kbm_kmer_t*, ITSELF);
typedef struct {
u8i off:40, cnt:24;
} kbm_kaux_t;
define_list(kbmkauxv, kbm_kaux_t);
typedef struct {
kbm_kmer_t *mer;
kbm_kaux_t *aux;
u4i kidx;
u4i off:24, dir:1, pdir:1, fine:1, closed:1, extra_bits1:4;
u4i qbidx;
u4i poffs[2];
u8i bidx, boff, bend;
//kbm_bmer_t *b, *end;
} kbm_ref_t;
define_list(kbmrefv, kbm_ref_t);
#if 0
#define heap_cmp_kbm_bmer(refs, a, b) num_cmpx(refs[a].b->bidx, refs[b].b->bidx, refs[a].poffs[refs[a].pdir], refs[b].poffs[refs[b].pdir])
#endif
#define heap_cmp_kbm_bmer(refs, a, b) num_cmpx(refs[a]->bidx, refs[b]->bidx, refs[a].poffs[refs[a].pdir], refs[b].poffs[refs[b].pdir])
typedef struct {
u4i koff;
u4i kcnt:8, kmat:9, boff:15; // offset from the start bin_idx
} kbm_cmer_t;
define_list(kbmcmerv, kbm_cmer_t);
static const kbm_cmer_t KBM_CMER_NULL = {0, 0, 0, 0};
typedef struct {
u8i beg:46, mat:16, bt:2;
b2i var;
u2i gap;
b4i score;
} kbm_cell_t;
static const kbm_cell_t KBM_CELL_NULL = {0, 0, 0, 0, 0, 0};
define_list(kbmcellv, kbm_cell_t);
typedef struct {
u8i beg, end;
u4i mat;
int score;
} kbm_path_t;
define_list(kbmpathv, kbm_path_t);
#define kbmpath_hashcode(E) E.beg
#define kbmpath_hashequals(E1, E2) (E1).beg == (E2).beg
define_hashset(kbmphash, kbm_path_t, kbmpath_hashcode, kbmpath_hashequals);
typedef struct {
u4i qidx:31, qdir:1;
u4i tidx:31, tdir:1;
u8i cgoff:40, cglen:24;
int qb, qe, tb, te;
int mat, cnt, aln, gap; // gap is counted in BINs
} kbm_map_t;
define_list(kbmmapv, kbm_map_t);
typedef struct {
int rd_len_order; // 0
int min_bin_degree; // 2
u4i ksize, psize; // 0, 21
u4i kmax, kmin, kmer_mod, ksampling; // 1000, 1, 4.0 * KBM_N_HASH, KBM_BSIZE
float ktop; // 0.05
// runtime
u4i strand_mask; // 3. 1: forward; 2: reverse; 3: both
int self_aln; // 0. 0: map to all; 1: only map to greater read_id; 2: itself but reverse complementary
int skip_contained; // 1
u2i max_bgap; // 4
u2i max_bvar; // 4
float max_gap; // 0.6
u8i max_bcnt; // 0xFFFF
int pgap, pvar; // -7, -21
u4i max_hit; // 1000
int min_aln, min_mat; // 2048/256, 200
float aln_var; // 0.25
float min_sim; // kmer similarity: 0.05
int test_mode; // see codes
} KBMPar;
static const obj_desc_t kbmpar_obj_desc = {"kbmpar_obj_desc", sizeof(KBMPar), 0, {}, {}, {}, NULL, NULL};
typedef struct {
u8i flags; // 64 bits, 0: mem_load all, 1: mem_load rdseqs+reads; 2: Single Hash Mode;3-63: unused
KBMPar *par;
BaseBank *rdseqs;
u8i avail_bases;
u4i avail_reads;
kbmreadv *reads;
cuhash *tag2idx;
kbmbinv *bins;
BitVec *binmarks;
kbmbmerv *seeds;
kbmbauxv *sauxs;
kbmhash *hashs[KBM_N_HASH];
kbmkauxv *kauxs[KBM_N_HASH];
} KBM;
static inline size_t kbm_obj_desc_cnt(void *kbm, int idx){
UNUSED(kbm);
if(idx == 8 || idx == 9) return KBM_N_HASH;
else return 1;
}
static inline void rebuild_tag2idx_kbm(void *kbm, size_t aux);
static const obj_desc_t kbm_obj_desc = {.tag = "kbm_obj_desc", .size = sizeof(KBM), .n_child = 10,
.mem_type = {1, 1, 1, 1, 1, 1, 1, 1, 2, 2},
.addr = {offsetof(KBM, par), offsetof(KBM, rdseqs), offsetof(KBM, reads), offsetof(KBM, tag2idx), offsetof(KBM, bins), offsetof(KBM, binmarks), offsetof(KBM, seeds), offsetof(KBM, sauxs), offsetof(KBM, hashs), offsetof(KBM, kauxs)},
.desc = {&kbmpar_obj_desc, &basebank_obj_desc, &kbmreadv_deep_obj_desc, &cuhash_obj_desc, &kbmbinv_obj_desc, &bitvec_obj_desc, &kbmbmerv_obj_desc, &kbmbauxv_obj_desc, &kbmhash_obj_desc, &kbmkauxv_obj_desc},
kbm_obj_desc_cnt, rebuild_tag2idx_kbm
};
// Please note that, kbm->tag2idx is not functional after mem_load, because we use cuhash_obj_desc instread of cuhash_deep_obj_desc
typedef struct {
#if 0
u4i poff, bidx;
u4i refidx:26, koff:6;
#endif
u4i poff;
u4i refidx;
u8i bidx:40, koff:24;
} kbm_dpe_t;
define_list(kbmdpev, kbm_dpe_t);
typedef struct {
kbmdpev *kms; // kmer offset in query and bidx
u4i km_len;
BitVec *cmask; // bit for kbm_cmer_t
kbmcmerv *cms;
u4v *coffs; // kbm_cmer_t offset for each bin
BitVec *rmask[2];
kbmcellv *cells[2];
Bit2Vec *bts; // back trace flag: 0: diagonal, 1: horizontal, 2: vertical
kbmphash *paths; // storing best unique paths by now
u8i boff;
u8i last_bidx;
} KBMDP;
typedef struct {
u8i kmer;
u4i off;
u4i kidx:30, dir:1, closed:1;
} kmer_off_t;
define_list(kmeroffv, kmer_off_t);
typedef struct {
KBM *kbm;
KBMPar *par; // can diff from kbm->par
char *qtag;
BaseBank *qseqs;
u8i qsoff;
u4i qlen, slen, qnbin, qnbit;
u4i qidx;
u8i bmin, bmax;
kmeroffv *koffs[2];
kbmrefv *refs;
u4v *rank, **heaps;
u4i nheap;
u4i hptr;
u2i *binmap;
u4i bmlen, bmoff, bmcnt;
kbmdpev *caches[2];
KBMDP *dps[2];
kbmmapv *hits;
BitsVec *cigars;
BitVec *solids;
String *str;
} KBMAux;
static inline KBMPar* init_kbmpar(){
KBMPar *par;
par = malloc(sizeof(KBMPar));
par->rd_len_order = 0;
par->min_bin_degree = 2;
par->ksize = 0;
par->psize = 21;
par->kmax = 1000;
par->kmin = 1;
par->kmer_mod = 4 * KBM_N_HASH;
par->ksampling = KBM_BSIZE;
par->ktop = 0.05;
par->strand_mask = 3;
par->self_aln = 0;
par->skip_contained = 1;
par->max_bgap = 4; // 4 * KBM_BIN_SIZE
par->max_bvar = 4;
par->max_bcnt = 0xFFFF;
par->max_gap = 0.6;
par->pgap = -7;
par->pvar = -21;
par->max_hit = 1000;
par->min_aln = 2048 / KBM_BIN_SIZE;
par->min_mat = 200;
par->min_sim = 0.05;
par->aln_var = 0.25;
par->test_mode = 0;
return par;
}
static inline void free_kbmpar(KBMPar *par){ free(par); }
static inline KBM* init_kbm(KBMPar *par){
KBM *kbm;
u4i i;
kbm = malloc(sizeof(KBM));
kbm->flags = 0;
kbm->par = par;
kbm->rdseqs = init_basebank();
kbm->avail_bases = 0;
kbm->avail_reads = 0;
kbm->reads = init_kbmreadv(64);
kbm->tag2idx = init_cuhash(1023);
kbm->bins = init_kbmbinv(64);
kbm->binmarks = init_bitvec(1024);
//kbm->kfs = NULL;
kbm->seeds = init_kbmbmerv(64);
kbm->sauxs = init_kbmbauxv(64);
for(i=0;i<KBM_N_HASH;i++) kbm->hashs[i] = init_kbmhash(1023);
for(i=0;i<KBM_N_HASH;i++) kbm->kauxs[i] = init_kbmkauxv(64);
return kbm;
}
static inline void free_kbm(KBM *kbm){
u4i i;
if(kbm->flags & 0x1) return;
if(kbm->flags & 0x2){
} else {
free_basebank(kbm->rdseqs);
for(i=0;i<kbm->reads->size;i++){
if(kbm->reads->buffer[i].tag) free(kbm->reads->buffer[i].tag);
}
free_kbmreadv(kbm->reads);
}
free_cuhash(kbm->tag2idx);
free_kbmbinv(kbm->bins);
free_bitvec(kbm->binmarks);
//if(kbm->kfs) free(kbm->kfs);
free_kbmbmerv(kbm->seeds);
free_kbmbauxv(kbm->sauxs);
for(i=0;i<KBM_N_HASH;i++) free_kbmhash(kbm->hashs[i]);
for(i=0;i<KBM_N_HASH;i++) free_kbmkauxv(kbm->kauxs[i]);
free(kbm);
}
static inline void reset_index_kbm(KBM *kbm){
u4i i;
if(kbm->flags & 0x04){
free_kbmhash(kbm->hashs[0]);
kbm->hashs[0] = init_kbmhash(1023);
free_kbmkauxv(kbm->kauxs[0]);
kbm->kauxs[0] = init_kbmkauxv(64);
} else {
for(i=0;i<KBM_N_HASH;i++){
free_kbmhash(kbm->hashs[i]);
kbm->hashs[i] = init_kbmhash(1023);
free_kbmkauxv(kbm->kauxs[i]);
kbm->kauxs[i] = init_kbmkauxv(64);
}
}
free_kbmbmerv(kbm->seeds);
kbm->seeds = init_kbmbmerv(64);
free_kbmbauxv(kbm->sauxs);
kbm->sauxs = init_kbmbauxv(64);
//zeros_bitvec(kbm->binmarks);
}
static inline void clear_kbm(KBM *kbm){
u4i i;
if(kbm->flags & 0x1) return;
if(kbm->flags & 0x2){
} else {
clear_basebank(kbm->rdseqs);
for(i=0;i<kbm->reads->size;i++){
if(kbm->reads->buffer[i].tag) free(kbm->reads->buffer[i].tag);
}
clear_kbmreadv(kbm->reads);
clear_cuhash(kbm->tag2idx);
}
clear_kbmbinv(kbm->bins);
clear_bitvec(kbm->binmarks);
for(i=0;i<KBM_N_HASH;i++){
free_kbmhash(kbm->hashs[i]);
kbm->hashs[i] = init_kbmhash(1023);
free_kbmkauxv(kbm->kauxs[i]);
kbm->kauxs[i] = init_kbmkauxv(64);
if(kbm->flags & 0x04) break;
}
clear_kbmbmerv(kbm->seeds);
clear_kbmbauxv(kbm->sauxs);
}
#define kbm_cvt_length(seqlen) ((seqlen) & (MAX_U8 << KBM_BIN_BITS))
static inline void push_kbm(KBM *kbm, char *tag, int taglen, char *seq, u4i seqlen){
kbm_read_t *rd;
char *ptr;
if(taglen){
ptr = malloc(taglen + 1);
memcpy(ptr, tag, taglen);
ptr[taglen] = 0;
} else {
ptr = NULL;
}
if(seqlen > KBM_MAX_RDLEN) seqlen = KBM_MAX_RDLEN;
seqlen = kbm_cvt_length(seqlen);
rd = next_ref_kbmreadv(kbm->reads);
rd->seqoff = (kbm->rdseqs->size >> KBM_BIN_BITS);
rd->flag = 0;
rd->binoff = 0;
rd->bincnt = seqlen / KBM_BIN_SIZE;
rd->closed = 0;
rd->tag = ptr;
seq2basebank(kbm->rdseqs, seq, seqlen);
}
static inline void bitpush_kbm(KBM *kbm, char *tag, int taglen, u8i *seqs, u8i seqoff, u4i seqlen){
kbm_read_t *rd;
char *ptr;
if(taglen){
ptr = malloc(taglen + 1);
memcpy(ptr, tag, taglen);
ptr[taglen] = 0;
} else {
ptr = NULL;
}
if(seqlen > KBM_MAX_RDLEN) seqlen = KBM_MAX_RDLEN;
seqlen = kbm_cvt_length(seqlen);
rd = next_ref_kbmreadv(kbm->reads);
rd->seqoff = (kbm->rdseqs->size >> KBM_BIN_BITS);
rd->flag = 0;
rd->binoff = 0;
rd->bincnt = seqlen / KBM_BIN_SIZE;
rd->closed = 0;
rd->tag = ptr;
fast_fwdbits2basebank(kbm->rdseqs, seqs, seqoff, seqlen);
}
// Please call no more than once
static inline u8i filter_reads_kbm(KBM *kbm, u8i retain_size, int strategy){
u8i m, beg, end, len;
if(kbm->reads->size == 0) return 0;
if(retain_size == 0 || retain_size >= kbm->rdseqs->size) return kbm->rdseqs->size;
if((kbm->flags & 0x2) == 0){
if(kbm->par->rd_len_order){
sort_array(kbm->reads->buffer, kbm->reads->size, kbm_read_t, num_cmpgt(b.bincnt, a.bincnt));
if(strategy == 0){ // longest
len = 0;
for(end=0;end<kbm->reads->size;end++){
len += kbm->reads->buffer[end].bincnt * KBM_BIN_SIZE;
if(len >= retain_size) break;
}
for(m=end;m<kbm->reads->size;m++) free(kbm->reads->buffer[m].tag);
kbm->reads->size = end;
} else if(strategy == 1){ // median
m = kbm->reads->size / 2;
len = kbm->reads->buffer[m].bincnt * KBM_BIN_SIZE;
end = m;
for(beg=0;beg<=m&&len<retain_size;beg++){
len += kbm->reads->buffer[m - beg].bincnt * KBM_BIN_SIZE;
len += kbm->reads->buffer[m + beg].bincnt * KBM_BIN_SIZE;
}
end = beg * 2;
beg = m - beg;
if(beg){
remove_array_kbmreadv(kbm->reads, 0, beg);
}
for(m=end;m<kbm->reads->size;m++) free(kbm->reads->buffer[m].tag);
kbm->reads->size = end;
} else {
return kbm->rdseqs->size;
}
return len;
} else {
return kbm->rdseqs->size;
}
} else {
return kbm->rdseqs->size;
}
}
static inline void ready_kbm(KBM *kbm){
kbm_read_t *rd;
u4i i, j;
if((kbm->flags & 0x2) == 0){
if(kbm->par->rd_len_order){
sort_array(kbm->reads->buffer, kbm->reads->size, kbm_read_t, num_cmpgt(b.bincnt, a.bincnt));
}
encap_basebank(kbm->rdseqs, KBM_BSIZE);
}
clear_kbmbinv(kbm->bins);
for(i=0;i<kbm->reads->size;i++){
rd = ref_kbmreadv(kbm->reads, i);
if(rd->tag) put_cuhash(kbm->tag2idx, (cuhash_t){rd->tag, i});
if((kbm->flags & 0x2) == 0) rd->binoff = kbm->bins->size;
for(j=0;j<rd->bincnt;j++){
push_kbmbinv(kbm->bins, (kbm_bin_t){i, j, 0, 0});
}
if((kbm->flags & 0x2) == 0) rd->bincnt = j;
}
clear_bitvec(kbm->binmarks);
encap_bitvec(kbm->binmarks, kbm->bins->size);
kbm->binmarks->n_bit = kbm->bins->size;
zeros_bitvec(kbm->binmarks);
}
// Share seqs, reads
static inline KBM* clone_seqs_kbm(KBM *src, KBMPar *par){
KBM *dst;
dst = init_kbm(par);
free_basebank(dst->rdseqs);
free_kbmreadv(dst->reads);
dst->rdseqs = src->rdseqs;
dst->reads = src->reads;
dst->flags = 1LLU << 1;
ready_kbm(dst); // Notice encap_basebank in ready_kbm
return dst;
}
// rs[0]->n_head MUST >= 1
static inline void split_FIXP_kmers_kbm(BaseBank *rdseqs, u8i offset, u4i length, u1i ksize, u1i psize, u4i kmod, kmeroffv *rs[2]){
kmer_off_t *kp;
u8i kmer, krev, hv, npz, kmask, p, pmask;
u4i ki, npl;
int i, j;
u1i c, b, kshift, pshift, kpshf;
clear_kmeroffv(rs[0]);
clear_kmeroffv(rs[1]);
kshift = (ksize - 1) << 1;
kmask = (1LLU << (ksize << 1)) - 1LLU;
pshift = (psize - 1) << 1;
pmask = (1LLU << (psize << 1)) - 1LLU;
kpshf = psize << 1;
if(ksize){
// scan F-part of kmers
kmer = krev = 0;
for(i=0;i+1<ksize;i++){
c = bits2bit(rdseqs->bits, offset + i);
kmer = (kmer << 2) | c;
krev = (krev >> 2) | (((u8i)((~c) & 0x3)) << kshift);
}
for(;i<(int)length;i++){
c = bits2bit(rdseqs->bits, offset + i);
kmer = ((kmer << 2) | c) & kmask;
krev = (krev >> 2) | (((u8i)((~c) & 0x3)) << kshift);
if(kmer < krev){
push_kmeroffv(rs[0], (kmer_off_t){kmer, i - (ksize - 1), 0, 0, 1});
} else if(krev < kmer){
push_kmeroffv(rs[1], (kmer_off_t){krev, i - (ksize - 1), 0, 1, 1});
}
}
if(psize){
// scan P-part of forward kmers
assert(rs[0]->n_head > 0);
memset(rs[0]->buffer - 1, 0, sizeof(kmer_off_t)); // rs[0]->n_head > 0
rs[0]->buffer[-1].off = length;
npz = 0;
npl = 0;
kp = rs[0]->buffer + rs[0]->size - 1;
b = 4;
for(i=length-1;i>=0;i--){
if(kp->off + (ksize - 1) == (u4i)i){
if(npl >= psize){
p = npz & pmask;
kp->closed = 0;
kp->kmer = (kp->kmer << kpshf) | p;
}
kp --;
}
c = bits2revbit(rdseqs->bits, offset + i);
if(c == b){
} else {
npz = (npz << 2) | c;
npl ++;
b = c;
}
}
// scan P-part of reverse kmers
encap_kmeroffv(rs[1], 1); memset(rs[1]->buffer + rs[1]->size, 0xFF, sizeof(kmer_off_t));
npz = 0;
npl = 0;
kp = rs[1]->buffer;
b = 4;
for(i=0;i<(int)length;i++){
if(kp->off == (u4i)(i)){
if(npl >= psize){
p = npz & pmask;
kp->closed = 0;
kp->kmer = (kp->kmer << kpshf) | p;
kp->off = kp->off - psize;
}
kp ++;
}
c = bits2bit(rdseqs->bits, offset + i);
if(c == b){
} else {
npz = (npz << 2) | c;
npl ++;
b = c;
}
}
} else {
for(i=0;(u4i)i<rs[0]->size;i++) rs[0]->buffer[i].closed = 0;
for(i=0;(u4i)i<rs[1]->size;i++) rs[1]->buffer[i].closed = 0;
}
} else if(psize){
kmer = krev = 0;
b = 4;
for(i=j=0;i<(int)length;i++){
c = bits2bit(rdseqs->bits, offset + i);
if(b == c) continue;
b = c;
kmer = ((kmer << 2) | c) & pmask;
krev = (krev >> 2) | (((u8i)((~c) & 0x3)) << pshift);
j ++;
if(j < psize) continue;
if(kmer < krev){
push_kmeroffv(rs[0], (kmer_off_t){kmer, i - (psize - 1), 0, 0, 0});
} else if(krev < kmer){
push_kmeroffv(rs[1], (kmer_off_t){krev, i - (psize - 1), 0, 1, 0});
}
}
}
for(b=0;b<2;b++){
for(i=0;(u4i)i<rs[b]->size;i++){
if(rs[b]->buffer[i].closed) continue;
hv = kbm_kmer_smear(rs[b]->buffer[i].kmer);
ki = hv % kmod;
if(ki >= KBM_N_HASH) rs[b]->buffer[i].closed = 1;
rs[b]->buffer[i].kidx = ki;
}
}
}
static inline u8i seed2solid_idx_kbm(KBM *kbm, kbm_dpe_t *p){
kbm_bin_t *b;
kbm_read_t *rd;
u8i seqoff;
b = kbm->bins->buffer + p->bidx;
rd = kbm->reads->buffer + b->ridx;
seqoff = (((rd->seqoff + b->off) * KBM_BSIZE) >> 1) + p->koff;
return seqoff;
}
static inline u8i rdoff2solid_idx_kbm(KBM *kbm, u4i ridx, u4i roff){
kbm_read_t *rd;
u8i seqoff;
rd = kbm->reads->buffer + ridx;
seqoff = (rd->seqoff * KBM_BIN_SIZE + roff) >> 1;
return seqoff;
}
#define binoff2solid_koff_kbm(kbm, bidx, boff) ((boff) >> 1)
typedef struct {
u8i mer:50, kidx:14;
u8i bidx;
u4i cnt:22, koff:8, dir:1, used:1;
} kbm_midx_t;
define_list(kbmmidxv, kbm_midx_t);
typedef struct {
u8i bidx;
kbm_baux_t aux;
} kbm_tmp_bmer_t;
define_list(tmpbmerv, kbm_tmp_bmer_t);
thread_beg_def(midx);
KBM *kbm;
u8i beg, end; // (end - beg) * KBM_BSIZE MUST <= KBM_KMEROFF_MAX
u8i ktot, nrem, Nrem, none, nflt, offset;
u8i srem, Srem;
u8i *cnts, n_cnt;
int task;
int cal_degree;
pthread_mutex_t *locks;
thread_end_def(midx);
thread_beg_func(midx);
KBM *kbm;
kbm_bin_t *bin;
kbmmidxv **kidxs;
kbm_midx_t *mx;
kmer_off_t *f;
kbm_kmer_t *u;
kbm_kaux_t *x;
kmeroffv *kmers[2];
tmpbmerv *bms;
u8i bidx, off;
u4i i, j, k, len, ncpu, tidx, kidx;
int exists;
kbm = midx->kbm;
ncpu = midx->n_cpu;
tidx = midx->t_idx;
kmers[0] = adv_init_kmeroffv(64, 0, 1);
kmers[1] = adv_init_kmeroffv(64, 0, 1);
kidxs = malloc(KBM_N_HASH * sizeof(kbmmidxv*));
for(i=0;i<KBM_N_HASH;i++) kidxs[i] = init_kbmmidxv(64);
bms = init_tmpbmerv(KBM_MAX_KCNT);
thread_beg_loop(midx);
if(midx->task == 1){
// counting kmers
for(i=0;i<KBM_N_HASH;i++) clear_kbmmidxv(kidxs[i]);
for(bidx=midx->beg+tidx;bidx<midx->end;bidx+=ncpu){
if(KBM_LOG == 0 && tidx == 0 && ((bidx - midx->beg) % 100000) == 0){ fprintf(KBM_LOGF, "\r%llu", bidx - midx->beg); fflush(KBM_LOGF); }
bin = ref_kbmbinv(kbm->bins, bidx);
if(bin->closed) continue;
off = (kbm->reads->buffer[bin->ridx].seqoff + bin->off) * KBM_BIN_SIZE;
len = KBM_BIN_SIZE;
split_FIXP_kmers_kbm(kbm->rdseqs, off, len, kbm->par->ksize, kbm->par->psize, kbm->par->kmer_mod, kmers);
for(i=0;i<2;i++){
for(j=0;j<kmers[i]->size;j++){
f = ref_kmeroffv(kmers[i], j);
if(f->closed) continue;
mx = next_ref_kbmmidxv(kidxs[f->kidx]);
mx->mer = f->kmer;
mx->kidx = f->kidx;
mx->bidx = bidx;
mx->dir = i;
mx->koff = f->off;
if(kidxs[f->kidx]->size >= 64){
kidx = f->kidx;
// lock hashs[kidx]
pthread_mutex_lock(midx->locks + kidx);
// hash adding
for(k=0;k<kidxs[kidx]->size;k++){
mx = ref_kbmmidxv(kidxs[kidx], k);
u = prepare_kbmhash(kbm->hashs[kidx], mx->mer, &exists);
if(exists){
if(u->tot < KBM_MAX_KCNT) u->tot ++;
} else {
u->mer = mx->mer;
u->tot = 1;
u->flt = 0;
}
}
// free hashs[f->kidx]
pthread_mutex_unlock(midx->locks + kidx);
clear_kbmmidxv(kidxs[kidx]);
}
}
}
}
for(kidx=0;kidx<KBM_N_HASH;kidx++){
if(kidxs[kidx]->size){
// lock hashs[kidx]
pthread_mutex_lock(midx->locks + kidx);
// hash adding
for(k=0;k<kidxs[kidx]->size;k++){
mx = ref_kbmmidxv(kidxs[kidx], k);
u = prepare_kbmhash(kbm->hashs[kidx], mx->mer, &exists);
if(exists){
if(u->tot < KBM_MAX_KCNT) u->tot ++;
} else {
u->mer = mx->mer;
u->tot = 1;
u->flt = 0;
}
}
// free hashs[f->kidx]
pthread_mutex_unlock(midx->locks + kidx);
clear_kbmmidxv(kidxs[kidx]);
}
}
} else if(midx->task == 2){
// delete low freq kmers
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
reset_iter_kbmhash(kbm->hashs[i]);
while((u = ref_iter_kbmhash(kbm->hashs[i]))){
if(u->tot < kbm->par->kmin){
delete_kbmhash(kbm->hashs[i], u);
}
}
}
} else if(midx->task == 3){
// stat kmer counts
memset(midx->cnts, 0, midx->n_cnt * sizeof(u8i));
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
reset_iter_kbmhash(kbm->hashs[i]);
while((u = ref_iter_kbmhash(kbm->hashs[i]))){
midx->cnts[num_min(midx->n_cnt, u->tot) - 1] ++;
}
}
} else if(midx->task == 4){
// stat counts
midx->offset = 0;
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
reset_iter_kbmhash(kbm->hashs[i]);
while((u = ref_iter_kbmhash(kbm->hashs[i]))){
x = ref_kbmkauxv(kbm->kauxs[i], offset_kbmhash(kbm->hashs[i], u));
x->off = midx->offset;
x->cnt = 0;
midx->ktot += u->tot;
if(u->tot < kbm->par->kmin){
u->flt = 1;
} else if(u->tot > kbm->par->kmax){
u->flt = 1;
} else {
midx->offset += u->tot;
}
}
}
} else if(midx->task == 5){
// revise offset
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
for(off=0;off<kbm->kauxs[i]->size;off++) kbm->kauxs[i]->buffer[off].off += midx->offset;
}
} else if(midx->task == 6){
// fill seeds
for(i=0;i<KBM_N_HASH;i++) clear_kbmmidxv(kidxs[i]);
u4v *chgs;
chgs = init_u4v(KBM_BSIZE);
for(bidx=midx->beg+tidx;bidx<midx->end;bidx+=ncpu){
if(KBM_LOG == 0 && tidx == 0 && ((bidx - midx->beg) % 100000) == 0){ fprintf(KBM_LOGF, "\r%llu", bidx - midx->beg); fflush(KBM_LOGF); }
bin = ref_kbmbinv(kbm->bins, bidx);
if(bin->closed) continue;
bin->degree = 0;
off = (kbm->reads->buffer[bin->ridx].seqoff + bin->off) * KBM_BIN_SIZE;
len = KBM_BIN_SIZE;
split_FIXP_kmers_kbm(kbm->rdseqs, off, len, kbm->par->ksize, kbm->par->psize, kbm->par->kmer_mod, kmers);
clear_u4v(chgs);
for(i=0;i<2;i++){
for(j=0;j<kmers[i]->size;j++){
f = ref_kmeroffv(kmers[i], j);
if(f->closed) continue;
mx = next_ref_kbmmidxv(kidxs[f->kidx]);
mx->mer = f->kmer;
mx->kidx = f->kidx;
mx->bidx = bidx;
mx->dir = i;
mx->koff = f->off;
if(kidxs[f->kidx]->size == 64){
push_u4v(chgs, f->kidx);
}
}
}
for(i=0;i<chgs->size;i++){
kidx = chgs->buffer[i];
if(kidxs[kidx]->size == 0) continue;
pthread_mutex_lock(midx->locks + kidx);
for(k=0;k<kidxs[kidx]->size;k++){
mx = ref_kbmmidxv(kidxs[kidx], k);
u = get_kbmhash(kbm->hashs[kidx], mx->mer);
if(u && u->flt == 0){
x = ref_kbmkauxv(kbm->kauxs[kidx], offset_kbmhash(kbm->hashs[kidx], u));
kbm->bins->buffer[mx->bidx].degree ++;
if(x->cnt < u->tot){
if(x->cnt && getval_bidx(kbm, x->off + x->cnt - 1) == mx->bidx && kbm->sauxs->buffer[x->off + x->cnt - 1].dir == mx->dir){
// repeated kmer within one bin
} else {
kbm->seeds->buffer[x->off + x->cnt].bidx = mx->bidx & MAX_U4;
kbm->sauxs->buffer[x->off + x->cnt].bidx = mx->bidx >> 32;
kbm->sauxs->buffer[x->off + x->cnt].dir = mx->dir;
kbm->sauxs->buffer[x->off + x->cnt].koff = mx->koff >> 1;
x->cnt ++;
}
}
}
}
pthread_mutex_unlock(midx->locks + kidx);
clear_kbmmidxv(kidxs[kidx]);
}
}
for(kidx=0;kidx<KBM_N_HASH;kidx++){
if(kidxs[kidx]->size){
// lock hashs[kidx]
pthread_mutex_lock(midx->locks + kidx);
// hash adding
for(k=0;k<kidxs[kidx]->size;k++){
mx = ref_kbmmidxv(kidxs[kidx], k);
u = get_kbmhash(kbm->hashs[kidx], mx->mer);
if(u && u->flt == 0){
x = ref_kbmkauxv(kbm->kauxs[kidx], offset_kbmhash(kbm->hashs[kidx], u));
kbm->bins->buffer[mx->bidx].degree ++;
if(x->cnt < u->tot){
if(x->cnt && getval_bidx(kbm, x->off + x->cnt - 1) == mx->bidx && kbm->sauxs->buffer[x->off + x->cnt - 1].dir == mx->dir){
// repeated kmer within one bin
} else {
kbm->seeds->buffer[x->off + x->cnt].bidx = mx->bidx & MAX_U4;
kbm->sauxs->buffer[x->off + x->cnt].bidx = mx->bidx >> 32;
kbm->sauxs->buffer[x->off + x->cnt].dir = mx->dir;
kbm->sauxs->buffer[x->off + x->cnt].koff = mx->koff >> 1;
x->cnt ++;
}
}
}
}
// free hashs[f->kidx]
pthread_mutex_unlock(midx->locks + kidx);
clear_kbmmidxv(kidxs[kidx]);
}
}
free_u4v(chgs);
} else if(midx->task == 7){
// count added kmers
midx->srem = midx->Srem = 0;
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
reset_iter_kbmhash(kbm->hashs[i]);
while((u = ref_iter_kbmhash(kbm->hashs[i]))){
x = ref_kbmkauxv(kbm->kauxs[i], offset_kbmhash(kbm->hashs[i], u));
if(x->cnt){
midx->srem ++;
midx->Srem += x->cnt;
}
}
}
} else if(midx->task == 8){
// sort seeds within a kmer
for(i=tidx;i<KBM_N_HASH;i+=ncpu){
reset_iter_kbmhash(kbm->hashs[i]);
while((u = ref_iter_kbmhash(kbm->hashs[i]))){
x = ref_kbmkauxv(kbm->kauxs[i], offset_kbmhash(kbm->hashs[i], u));
if(x->cnt < 2) continue;
clear_tmpbmerv(bms);
for(j=0;j<x->cnt;j++){
push_tmpbmerv(bms, (kbm_tmp_bmer_t){getval_bidx(kbm, x->off + j), kbm->sauxs->buffer[x->off + j]});
}
sort_array(bms->buffer, bms->size, kbm_tmp_bmer_t, num_cmpgt(a.bidx, b.bidx));
kbm->seeds->buffer[x->off + 0].bidx = bms->buffer[0].bidx & MAX_U4;
kbm->sauxs->buffer[x->off + 0].bidx = bms->buffer[0].bidx >> 32;
kbm->sauxs->buffer[x->off + 0] = bms->buffer[0].aux;
len = 1;
for(j=1;j<x->cnt;j++){
if(bms->buffer[j].bidx < bms->buffer[j - 1].bidx){
continue;
}
kbm->seeds->buffer[x->off + len].bidx = bms->buffer[j].bidx & MAX_U4;
kbm->sauxs->buffer[x->off + len].bidx = bms->buffer[0].bidx >> 32;
kbm->sauxs->buffer[x->off + len] = bms->buffer[j].aux;
len ++;
}
x->cnt = len;
}
}
}
thread_end_loop(midx);
free_kmeroffv(kmers[0]);
free_kmeroffv(kmers[1]);
for(i=0;i<KBM_N_HASH;i++) free_kbmmidxv(kidxs[i]);
free(kidxs);
free_tmpbmerv(bms);
thread_end_func(midx);
static inline void index_kbm(KBM *kbm, u8i beg, u8i end, u4i ncpu, FILE *kmstat){
u8i ktyp, nflt, nrem, Nrem, none, ktot, srem, Srem, off, cnt, *kcnts, MAX;
u8i i, b, e, n;
u4i j, kavg, batch_size;
pthread_mutex_t *hash_locks;
thread_preprocess(midx);
batch_size = 10000;
clear_kbmbmerv(kbm->seeds);
for(i=0;i<KBM_N_HASH;i++) clear_kbmhash(kbm->hashs[i]);
kcnts = NULL;
MAX = KBM_MAX_KCNT;
hash_locks = calloc(KBM_N_HASH, sizeof(pthread_mutex_t));
thread_beg_init(midx, ncpu);
midx->kbm = kbm;
midx->beg = beg;
midx->end = end;
midx->cnts = NULL;
midx->n_cnt = MAX;
midx->task = 0;
midx->cal_degree = 0;
midx->locks = hash_locks;
thread_end_init(midx);
fprintf(KBM_LOGF, "[%s] - scanning kmers (K%dP%dS%0.2f) from %llu bins\n", date(), kbm->par->ksize, kbm->par->psize, 1.0 * kbm->par->kmer_mod / KBM_N_HASH, end - beg);
b = e = beg;
thread_apply_all(midx, midx->task = 1);
if(KBM_LOG == 0){ fprintf(KBM_LOGF, "\r%llu bins\n", end - beg); fflush(KBM_LOGF); }
kcnts = calloc(MAX, sizeof(u8i));
thread_beg_iter(midx);
midx->cnts = calloc(MAX, sizeof(u8i));
midx->task = 3; // counting raw kmers
thread_wake(midx);
thread_end_iter(midx);
thread_beg_iter(midx);
thread_wait(midx);
for(i=0;i<MAX;i++) kcnts[i] += midx->cnts[i];
thread_end_iter(midx);
if(kmstat){
fprintf(kmstat, "#Reads: %llu\n", (u8i)kbm->reads->size);
fprintf(kmstat, "#Bases: %llu bp\n", (u8i)kbm->rdseqs->size);
fprintf(kmstat, "#K%dP%dS%0.2f\n", kbm->par->ksize, kbm->par->psize, 1.0 * kbm->par->kmer_mod / KBM_N_HASH);
for(i=0;i+1<MAX;i++){
fprintf(kmstat, "%llu\t%llu\t%llu\n", i + 1, kcnts[i], (i + 1) * kcnts[i]);
}
fflush(kmstat);
}
if(kmstat){
u8i *_kcnts;
_kcnts = malloc(200 * sizeof(u8i));
for(i=0;i<200;i++){
_kcnts[i] = (i + 1) * kcnts[i];
}
char *txt = barplot_txt_u8_simple(100, 20, _kcnts, 200, 0);
fprintf(KBM_LOGF, "********************** Kmer Frequency **********************\n");
fputs(txt, KBM_LOGF);
fprintf(KBM_LOGF, "********************** 1 - 201 **********************\n");
ktyp = 0;
for(i=0;i<MAX;i++){
ktyp += (i + 1) * kcnts[i];
}