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map.c
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map.c
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#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <errno.h>
#include "kthread.h"
#include "kvec.h"
#include "kalloc.h"
#include "sdust.h"
#include "mmpriv.h"
#include "bseq.h"
#include "khash.h"
struct mm_tbuf_s {
void *km;
int rep_len, frag_gap; // updated per read.
double timers[MM_N_THR_TIMERS];
}; // per thread
#if defined(__AMD_SPLIT_KERNELS__)
#include "plutils.h"
#define N_ACCUM 64
typedef struct{
int batchid;
void *km; // memory pool for each batch
int count; // number of reads in the batch
size_t total_n; // total number of anchors in the batch
chain_read_t *reads;
} mm_batch_trbuf_t;
// local variables required for each read processed by a CPU thread
typedef struct {
mm_batch_trbuf_t acc_batch;
int is_full;
mm_batch_trbuf_t launched_batch;
int has_launched;
mm_batch_trbuf_t pending_batch;
int is_pending;
} mm_trbuf_t; // per thread
#endif
mm_tbuf_t *mm_tbuf_init(void)
{
mm_tbuf_t *b;
b = (mm_tbuf_t*)calloc(1, sizeof(mm_tbuf_t));
if (!(mm_dbg_flag & 1)) b->km = km_init();
return b;
}
void mm_tbuf_destroy(mm_tbuf_t *b)
{
if (b == 0) return;
km_destroy(b->km);
free(b);
}
void *mm_tbuf_get_km(mm_tbuf_t *b)
{
return b->km;
}
#if defined(__AMD_SPLIT_KERNELS__)
void mm_trbuf_batch_init(mm_batch_trbuf_t *batch_, int batch_max_reads) {
batch_->count = 0;
batch_->total_n = 0;
batch_->reads = (chain_read_t *)malloc(sizeof(chain_read_t) * batch_max_reads);
memset(batch_->reads, 0, sizeof(chain_read_t) * batch_max_reads);
batch_->batchid = -1;
batch_->km = km_init();
}
void mm_trbuf_batch_reset(mm_batch_trbuf_t *batch_, int batch_max_reads, const mm_mapopt_t *opt) {
// free all the reads in the batch
for (int i = 0; i < batch_->count; i++) {
free_read(&batch_->reads[i], batch_->km);
}
/* reset memory pool km */
km_stat_t kmst;
if (batch_->km) {
chain_read_t *last_read = batch_->reads + batch_->count;
km_stat(batch_->km, &kmst);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "QM\t%s\t%d\tBid=%d\tcap=%ld,avail=%ld,nCore=%ld,largest=%ld\n",
last_read->seq.name, last_read->seq.qlen_sum, batch_->batchid, kmst.capacity, kmst.available, kmst.n_cores, kmst.largest);
assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak
assert(kmst.capacity == kmst.meta_size + kmst.available);
if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) {
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "[W::%s] reset thread-local memory after read %s\n", __func__, last_read->seq.name);
km_destroy(batch_->km);
batch_->km = km_init();
}
}
batch_->count = 0;
batch_->total_n = 0;
batch_->batchid = -1;
}
void mm_trbuf_batch_destroy(mm_batch_trbuf_t *batch_){
// free reads in the batch
for (int i = 0; i < batch_->count; i++){
free_read(&batch_->reads[i], batch_->km);
}
batch_->batchid = -1;
batch_->total_n = 0;
batch_->count = 0;
/* clean memory pool */
km_stat_t kmst;
if (batch_->km) {
km_stat(batch_->km, &kmst);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "Destroy memory pool cap=%ld,avail=%ld,nCore=%ld,largest=%ld\n",
kmst.capacity, kmst.available, kmst.n_cores, kmst.largest);
assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak
assert(kmst.capacity == kmst.meta_size + kmst.available);
km_destroy(batch_->km);
batch_->km = 0;
}
free(batch_->reads);
batch_->reads = 0;
}
mm_trbuf_t *mm_trbuf_init(const int batch_max_reads, const mm_mapopt_t *opt)
{
mm_trbuf_t *tr;
tr = (mm_trbuf_t *)calloc(1, sizeof(mm_trbuf_t));
tr->is_full = 0;
tr->is_pending = 0;
tr->has_launched = 0;
mm_trbuf_batch_init(&tr->acc_batch, batch_max_reads);
tr->acc_batch.batchid = 0;
mm_trbuf_batch_init(&tr->pending_batch, batch_max_reads);
tr->pending_batch.batchid = 1;
mm_trbuf_batch_init(&tr->launched_batch, batch_max_reads);
tr->launched_batch.batchid = 2;
return tr;
}
void mm_trbuf_destroy(mm_trbuf_t *tr)
{
if (tr == 0) return;
mm_trbuf_batch_destroy(&tr->acc_batch);
mm_trbuf_batch_destroy(&tr->pending_batch);
mm_trbuf_batch_destroy(&tr->launched_batch);
free(tr);
}
#endif
static int mm_dust_minier(void *km, int n, mm128_t *a, int l_seq, const char *seq, int sdust_thres)
{
int n_dreg, j, k, u = 0;
const uint64_t *dreg;
sdust_buf_t *sdb;
if (sdust_thres <= 0) return n;
sdb = sdust_buf_init(km);
dreg = sdust_core((const uint8_t*)seq, l_seq, sdust_thres, 64, &n_dreg, sdb);
for (j = k = 0; j < n; ++j) { // squeeze out minimizers that significantly overlap with LCRs
int32_t qpos = (uint32_t)a[j].y>>1, span = a[j].x&0xff;
int32_t s = qpos - (span - 1), e = s + span;
while (u < n_dreg && (int32_t)dreg[u] <= s) ++u;
if (u < n_dreg && (int32_t)(dreg[u]>>32) < e) {
int v, l = 0;
for (v = u; v < n_dreg && (int32_t)(dreg[v]>>32) < e; ++v) { // iterate over LCRs overlapping this minimizer
int ss = s > (int32_t)(dreg[v]>>32)? s : dreg[v]>>32;
int ee = e < (int32_t)dreg[v]? e : (uint32_t)dreg[v];
l += ee - ss;
}
if (l <= span>>1) a[k++] = a[j]; // keep the minimizer if less than half of it falls in masked region
} else a[k++] = a[j];
}
sdust_buf_destroy(sdb);
return k; // the new size
}
static void collect_minimizers(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, mm128_v *mv)
{
int i, n, sum = 0;
mv->n = 0;
for (i = n = 0; i < n_segs; ++i) {
size_t j;
mm_sketch(km, seqs[i], qlens[i], mi->w, mi->k, i, mi->flag&MM_I_HPC, mv);
for (j = n; j < mv->n; ++j)
mv->a[j].y += sum << 1;
if (opt->sdust_thres > 0) // mask low-complexity minimizers
mv->n = n + mm_dust_minier(km, mv->n - n, mv->a + n, qlens[i], seqs[i], opt->sdust_thres);
sum += qlens[i], n = mv->n;
}
}
#include "ksort.h"
#define heap_lt(a, b) ((a).x > (b).x)
KSORT_INIT(heap, mm128_t, heap_lt)
static inline int skip_seed(int flag, uint64_t r, const mm_seed_t *q, const char *qname, int qlen, const mm_idx_t *mi, int *is_self)
{
*is_self = 0;
if (qname && (flag & (MM_F_NO_DIAG|MM_F_NO_DUAL))) {
const mm_idx_seq_t *s = &mi->seq[r>>32];
int cmp;
cmp = strcmp(qname, s->name);
if ((flag&MM_F_NO_DIAG) && cmp == 0 && (int)s->len == qlen) {
if ((uint32_t)r>>1 == (q->q_pos>>1)) return 1; // avoid the diagnonal anchors
if ((r&1) == (q->q_pos&1)) *is_self = 1; // this flag is used to avoid spurious extension on self chain
}
if ((flag&MM_F_NO_DUAL) && cmp > 0) // all-vs-all mode: map once
return 1;
}
if (flag & (MM_F_FOR_ONLY|MM_F_REV_ONLY)) {
if ((r&1) == (q->q_pos&1)) { // forward strand
if (flag & MM_F_REV_ONLY) return 1;
} else {
if (flag & MM_F_FOR_ONLY) return 1;
}
}
return 0;
}
static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len,
int *n_mini_pos, uint64_t **mini_pos)
{
int i, n_m, heap_size = 0;
int64_t j, n_for = 0, n_rev = 0;
mm_seed_t *m;
mm128_t *a, *heap;
m = mm_collect_matches(km, &n_m, qlen, max_occ, opt->max_max_occ, opt->occ_dist, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
heap = (mm128_t*)kmalloc(km, n_m * sizeof(mm128_t));
a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
for (i = 0, heap_size = 0; i < n_m; ++i) {
if (m[i].n > 0) {
heap[heap_size].x = m[i].cr[0];
heap[heap_size].y = (uint64_t)i<<32;
++heap_size;
}
}
ks_heapmake_heap(heap_size, heap);
while (heap_size > 0) {
mm_seed_t *q = &m[heap->y>>32];
mm128_t *p;
uint64_t r = heap->x;
int32_t is_self, rpos = (uint32_t)r >> 1;
if (!skip_seed(opt->flag, r, q, qname, qlen, mi, &is_self)) {
if ((r&1) == (q->q_pos&1)) { // forward strand
p = &a[n_for++];
p->x = (r&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
} else { // reverse strand
p = &a[(*n_a) - (++n_rev)];
p->x = 1ULL<<63 | (r&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
}
p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
if (q->is_tandem) p->y |= MM_SEED_TANDEM;
if (is_self) p->y |= MM_SEED_SELF;
}
// update the heap
if ((uint32_t)heap->y < q->n - 1) {
++heap[0].y;
heap[0].x = m[heap[0].y>>32].cr[(uint32_t)heap[0].y];
} else {
heap[0] = heap[heap_size - 1];
--heap_size;
}
ks_heapdown_heap(0, heap_size, heap);
}
kfree(km, m);
kfree(km, heap);
// reverse anchors on the reverse strand, as they are in the descending order
for (j = 0; j < n_rev>>1; ++j) {
mm128_t t = a[(*n_a) - 1 - j];
a[(*n_a) - 1 - j] = a[(*n_a) - (n_rev - j)];
a[(*n_a) - (n_rev - j)] = t;
}
if (*n_a > n_for + n_rev) {
memmove(a + n_for, a + (*n_a) - n_rev, n_rev * sizeof(mm128_t));
*n_a = n_for + n_rev;
}
return a;
}
static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len,
int *n_mini_pos, uint64_t **mini_pos)
{
int i, n_m;
mm_seed_t *m;
mm128_t *a;
m = mm_collect_matches(km, &n_m, qlen, max_occ, opt->max_max_occ, opt->occ_dist, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
for (i = 0, *n_a = 0; i < n_m; ++i) {
mm_seed_t *q = &m[i];
const uint64_t *r = q->cr;
uint32_t k;
for (k = 0; k < q->n; ++k) {
int32_t is_self, rpos = (uint32_t)r[k] >> 1;
mm128_t *p;
if (skip_seed(opt->flag, r[k], q, qname, qlen, mi, &is_self)) continue;
p = &a[(*n_a)++];
if ((r[k]&1) == (q->q_pos&1)) { // forward strand
p->x = (r[k]&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
} else if (!(opt->flag & MM_F_QSTRAND)) { // reverse strand and not in the query-strand mode
p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
} else { // reverse strand; query-strand
int32_t len = mi->seq[r[k]>>32].len;
p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | (len - (rpos + 1 - q->q_span) - 1); // coordinate only accurate for non-HPC seeds
p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
}
p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
if (q->is_tandem) p->y |= MM_SEED_TANDEM;
if (is_self) p->y |= MM_SEED_SELF;
}
}
kfree(km, m);
radix_sort_128x(a, a + (*n_a));
return a;
}
static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
{
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
if (n_segs <= 1) mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 1, opt->max_gap * 0.8, n_regs, regs);
else mm_select_sub_multi(km, opt->pri_ratio, 0.2f, 0.7f, max_chain_gap_ref, mi->k*2, opt->best_n, n_segs, qlens, n_regs, regs);
}
}
static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *km, int qlen, const char *seq, int *n_regs, mm_reg1_t *regs, mm128_t *a)
{
if (!(opt->flag & MM_F_CIGAR)) return regs;
regs = mm_align_skeleton(km, opt, mi, qlen, seq, n_regs, regs, a); // this calls mm_filter_regs()
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
mm_set_parent(km, opt->mask_level, opt->mask_len, *n_regs, regs, opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop);
mm_select_sub(km, opt->pri_ratio, mi->k*2, opt->best_n, 0, opt->max_gap * 0.8, n_regs, regs);
mm_set_sam_pri(*n_regs, regs);
}
return regs;
}
#if defined(__AMD_SPLIT_KERNELS__)
void mm_map_seed(const mm_idx_t *mi, const mm_mapopt_t *opt,
chain_read_t *read_, mm_tbuf_t *b, void *km) {
int n_segs = read_->n_seg;
const int *qlens = read_->qlens;
const char **seqs = read_->qseqs;
const char *qname = read_->seq.name;
int *rep_len = &read_->rep_len;
int *qlen_sum = &read_->seq.qlen_sum;
int *n_mini_pos = &read_->n_mini_pos;
uint64_t **mini_pos = &read_->mini_pos;
int64_t *n_a = &read_->n;
mm128_t **a = &read_->a;
int i;
mm128_v mv = {0,0,0};
double *timers = b->timers;
double t1 = realtime();
for (i = 0, *qlen_sum = 0; i < n_segs; ++i) *qlen_sum += qlens[i];
if (*qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
if (opt->max_qlen > 0 && *qlen_sum > opt->max_qlen) return;
collect_minimizers(km, opt, mi, n_segs, qlens, seqs, &mv);
if (opt->q_occ_frac > 0.0f) mm_seed_mz_flt(km, &mv, opt->mid_occ, opt->q_occ_frac);
if (opt->flag & MM_F_HEAP_SORT) *a = collect_seed_hits_heap(km, opt, opt->mid_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
else *a = collect_seed_hits(km, opt, opt->mid_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
if (mm_dbg_flag & MM_DBG_PRINT_SEED) {
fprintf(stderr, "RS\t%d\n", *rep_len);
for (i = 0; i < *n_a; ++i)
fprintf(stderr, "SD\t%s\t%d\t%c\t%d\t%d\t%d\n", mi->seq[(*a)[i].x<<1>>33].name, (int32_t)(*a)[i].x, "+-"[(*a)[i].x>>63], (int32_t)(*a)[i].y, (int32_t)((*a)[i].y>>32&0xff),
i == 0? 0 : ((int32_t)(*a)[i].y - (int32_t)(*a)[i-1].y) - ((int32_t)(*a)[i].x - (int32_t)(*a)[i-1].x));
}
kfree(km, mv.a);
timers[MM_TIME_SEED] += realtime() - t1;
}
Misc build_misc(const mm_idx_t *mi, const mm_mapopt_t *opt, const int64_t qlen_sum, const int n_seg) {
int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
float chn_pen_gap, chn_pen_skip;
// set max chaining gap on the query and the reference sequence
if (is_sr)
max_chain_gap_qry = qlen_sum > opt->max_gap? qlen_sum : opt->max_gap;
else max_chain_gap_qry = opt->max_gap;
if (opt->max_gap_ref > 0) {
max_chain_gap_ref = opt->max_gap_ref; // always honor mm_mapopt_t::max_gap_ref if set
} else if (opt->max_frag_len > 0) {
max_chain_gap_ref = opt->max_frag_len - qlen_sum;
if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
} else max_chain_gap_ref = opt->max_gap;
chn_pen_gap = opt->chain_gap_scale * 0.01 * mi->k;
chn_pen_skip = opt->chain_skip_scale * 0.01 * mi->k;
Misc misc;
misc.max_iter = opt->max_chain_iter; // always set up MAX_UINT
misc.max_dist_y = max_chain_gap_qry;
misc.max_dist_x = max_chain_gap_ref;
misc.max_skip = opt->max_chain_skip;
misc.bw = opt->bw;
misc.min_cnt = opt->min_cnt;
misc.min_score = opt->min_chain_score;
misc.is_cdna = is_splice;
misc.n_seg = n_seg;
misc.chn_pen_gap = chn_pen_gap;
misc.chn_pen_skip = chn_pen_skip;
return misc;
}
void post_chaining_helper(const mm_idx_t *mi, const mm_mapopt_t *opt, chain_read_t* read, Misc misc, void *km) {
int n_segs = read->n_seg;
const char *qname = read->seq.name;
int *rep_len = &read->rep_len;
int *frag_gap = &read->frag_gap;
int *qlen_sum = &read->seq.qlen_sum;
int *n_regs0 = &read->n_u;
int *n_mini_pos = &read->n_mini_pos;
uint64_t **mini_pos = &read->mini_pos;
int64_t *n_a = &read->n;
uint64_t **u = &read->u;
mm128_t **a = &read->a;
int i;
mm128_v mv = {0, 0, 0};
if (opt->bw_long > opt->bw &&
(opt->flag & (MM_F_SPLICE | MM_F_SR | MM_F_NO_LJOIN)) == 0 &&
n_segs == 1 && *n_regs0 > 1) { // re-chain/long-join for long sequences
int32_t st = (int32_t)(*a)[0].y, en = (int32_t)(*a)[(int32_t)(*u)[0] - 1].y;
if (*qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > *qlen_sum * opt->rmq_rescue_ratio) {
int32_t i;
for (i = 0, *n_a = 0; i < *n_regs0; ++i) *n_a += (int32_t)(*u)[i];
kfree(km, *u);
radix_sort_128x(*a, (*a) + *n_a);
*a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
misc.chn_pen_gap, misc.chn_pen_skip, *n_a, *a, n_regs0, u, km);
}
}
else if (opt->max_occ > opt->mid_occ && *rep_len > 0 &&
!(opt->flag & MM_F_RMQ)) { // re-chain, mostly for short reads
int rechain = 0;
if (*n_regs0 > 0) { // test if the best chain has all the segments
int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
for (i = 0; i < *n_regs0; ++i) { // find the best chain
if (max < (int)((*u)[i]>>32)) max = (*u)[i]>>32, max_i = i, max_off = off;
off += (uint32_t)(*u)[i];
}
for (i = 1; i < (int32_t)(*u)[max_i]; ++i) // count the number of segments in the best chain
if (((*a)[max_off+i].y&MM_SEED_SEG_MASK) != ((*a)[max_off+i-1].y&MM_SEED_SEG_MASK))
++n_chained_segs;
if (n_chained_segs < n_segs)
rechain = 1;
} else rechain = 1;
if (rechain) { // redo chaining with a higher max_occ threshold
kfree(km, *a);
kfree(km, *u);
kfree(km, *mini_pos);
if (opt->flag & MM_F_HEAP_SORT) *a = collect_seed_hits_heap(km, opt, opt->max_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
else *a = collect_seed_hits(km, opt, opt->max_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
*a = mg_lchain_dp(misc.max_dist_x, misc.max_dist_y, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
misc.chn_pen_gap, misc.chn_pen_skip, misc.is_cdna, n_segs, *n_a, *a, n_regs0, u, km);
kfree(km, mv.a);
}
}
*frag_gap = misc.max_dist_x;
}
void mm_map_chain(const mm_idx_t *mi, const mm_mapopt_t *opt,
chain_read_t *read_, mm_tbuf_t *b, void *km) {
int n_segs = read_->n_seg;
const char *qname = read_->seq.name;
int *rep_len = &read_->rep_len;
int *frag_gap = &read_->frag_gap;
int *qlen_sum = &read_->seq.qlen_sum;
int *n_regs0 = &read_->n_u;
int *n_mini_pos = &read_->n_mini_pos;
uint64_t **mini_pos = &read_->mini_pos;
int64_t *n_a = &read_->n;
uint64_t **u = &read_->u;
mm128_t **a = &read_->a;
int i;
int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
mm128_v mv = {0,0,0};
float chn_pen_gap, chn_pen_skip;
double *timers = b->timers;
// set max chaining gap on the query and the reference sequence
if (is_sr)
max_chain_gap_qry = *qlen_sum > opt->max_gap? *qlen_sum : opt->max_gap;
else max_chain_gap_qry = opt->max_gap;
if (opt->max_gap_ref > 0) {
max_chain_gap_ref = opt->max_gap_ref; // always honor mm_mapopt_t::max_gap_ref if set
} else if (opt->max_frag_len > 0) {
max_chain_gap_ref = opt->max_frag_len - *qlen_sum;
if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
} else max_chain_gap_ref = opt->max_gap;
chn_pen_gap = opt->chain_gap_scale * 0.01 * mi->k;
chn_pen_skip = opt->chain_skip_scale * 0.01 * mi->k;
if (opt->flag & MM_F_RMQ) {
*a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, *n_a, *a, n_regs0, u, km);
} else {
*a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, is_splice, n_segs, *n_a, *a, n_regs0, u, km);
}
if (opt->bw_long > opt->bw && (opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && *n_regs0 > 1) { // re-chain/long-join for long sequences
int32_t st = (int32_t)(*a)[0].y, en = (int32_t)(*a)[(int32_t)(*u)[0] - 1].y;
if (*qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > *qlen_sum * opt->rmq_rescue_ratio) {
int32_t i;
for (i = 0, *n_a = 0; i < *n_regs0; ++i) *n_a += (int32_t)(*u)[i];
kfree(km, *u);
radix_sort_128x(*a, (*a) + *n_a);
*a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, *n_a, *a, n_regs0, u, km);
}
} else if (opt->max_occ > opt->mid_occ && *rep_len > 0 && !(opt->flag & MM_F_RMQ)) { // re-chain, mostly for short reads
int rechain = 0;
if (*n_regs0 > 0) { // test if the best chain has all the segments
int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
for (i = 0; i < *n_regs0; ++i) { // find the best chain
if (max < (int)((*u)[i]>>32)) max = (*u)[i]>>32, max_i = i, max_off = off;
off += (uint32_t)(*u)[i];
}
for (i = 1; i < (int32_t)(*u)[max_i]; ++i) // count the number of segments in the best chain
if (((*a)[max_off+i].y&MM_SEED_SEG_MASK) != ((*a)[max_off+i-1].y&MM_SEED_SEG_MASK))
++n_chained_segs;
if (n_chained_segs < n_segs)
rechain = 1;
} else rechain = 1;
if (rechain) { // redo chaining with a higher max_occ threshold
kfree(km, *a);
kfree(km, *u);
kfree(km, *mini_pos);
if (opt->flag & MM_F_HEAP_SORT) *a = collect_seed_hits_heap(km, opt, opt->max_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
else *a = collect_seed_hits(km, opt, opt->max_occ, mi, qname, &mv, *qlen_sum, n_a, rep_len, n_mini_pos, mini_pos);
*a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, is_splice, n_segs, *n_a, *a, n_regs0, u, km);
kfree(km, mv.a);
}
}
*frag_gap = max_chain_gap_ref;
}
void mm_map_align(const mm_idx_t *mi, const mm_mapopt_t *opt,
chain_read_t *read_, mm_reg1_t **regs, int *n_regs, mm_tbuf_t *b, void *km) {
int n_segs = read_->n_seg;
const int *qlens = read_->qlens;
const char **seqs = read_->qseqs;
const char *qname = read_->seq.name;
int rep_len = read_->rep_len;
int frag_gap = read_->frag_gap;
int qlen_sum = read_->seq.qlen_sum;
int *n_regs0 = &read_->n_u;
int n_mini_pos = read_->n_mini_pos;
uint64_t **mini_pos = &read_->mini_pos;
uint64_t *u = read_->u;
mm128_t *a = read_->a;
int i, j;
int max_chain_gap_ref = frag_gap;
int is_sr = !!(opt->flag & MM_F_SR);
uint32_t hash;
mm_reg1_t *regs0;
double *timers = b->timers;
double t1 = realtime();
for (i = 0; i < n_segs; ++i) n_regs[i] = 0, regs[i] = 0; // initialize regs
hash = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
hash = __ac_Wang_hash(hash);
regs0 = mm_gen_regs(km, hash, qlen_sum, *n_regs0, u, a, !!(opt->flag&MM_F_QSTRAND));
if (mi->n_alt) {
mm_mark_alt(mi, *n_regs0, regs0);
mm_hit_sort(km, n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
}
if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
for (j = 0; j < *n_regs0; ++j)
for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
i == regs0[j].as? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
chain_post(opt, max_chain_gap_ref, mi, km, qlen_sum, n_segs, qlens, n_regs0, regs0, a);
if (!is_sr && !(opt->flag&MM_F_QSTRAND)) {
mm_est_err(mi, qlen_sum, *n_regs0, regs0, a, n_mini_pos, *mini_pos);
*n_regs0 = mm_filter_strand_retained(*n_regs0, regs0);
}
if (n_segs == 1) { // uni-segment
regs0 = align_regs(opt, mi, km, qlens[0], seqs[0], n_regs0, regs0, a);
regs0 = (mm_reg1_t*)realloc(regs0, sizeof(*regs0) * *n_regs0);
mm_set_mapq(km, *n_regs0, regs0, opt->min_chain_score, opt->a, rep_len, is_sr);
n_regs[0] = *n_regs0, regs[0] = regs0;
} else { // multi-segment
mm_seg_t *seg;
seg = mm_seg_gen(km, hash, n_segs, qlens, *n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
free(regs0);
for (i = 0; i < n_segs; ++i) {
mm_set_parent(km, opt->mask_level, opt->mask_len, n_regs[i], regs[i], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); // update mm_reg1_t::parent
regs[i] = align_regs(opt, mi, km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
mm_set_mapq(km, n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr);
}
mm_seg_free(km, n_segs, seg);
if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
mm_pair(km, max_chain_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs); // pairing
}
timers[MM_TIME_ALIGN] += realtime() - t1;
kfree(km, a);
kfree(km, u);
kfree(km, *mini_pos);
}
#endif
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
int i, j, rep_len, qlen_sum, n_regs0, n_mini_pos;
int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
uint32_t hash;
int64_t n_a;
uint64_t *u, *mini_pos;
mm128_t *a;
mm128_v mv = {0,0,0};
mm_reg1_t *regs0;
km_stat_t kmst;
float chn_pen_gap, chn_pen_skip;
double *timers = b->timers;
double t1 = realtime();
for (i = 0, qlen_sum = 0; i < n_segs; ++i)
qlen_sum += qlens[i], n_regs[i] = 0, regs[i] = 0;
if (qlen_sum == 0 || n_segs <= 0 || n_segs > MM_MAX_SEG) return;
if (opt->max_qlen > 0 && qlen_sum > opt->max_qlen) return;
hash = qname && !(opt->flag & MM_F_NO_HASH_NAME)? __ac_X31_hash_string(qname) : 0;
hash ^= __ac_Wang_hash(qlen_sum) + __ac_Wang_hash(opt->seed);
hash = __ac_Wang_hash(hash);
collect_minimizers(b->km, opt, mi, n_segs, qlens, seqs, &mv);
if (opt->q_occ_frac > 0.0f) mm_seed_mz_flt(b->km, &mv, opt->mid_occ, opt->q_occ_frac);
if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else a = collect_seed_hits(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
if (mm_dbg_flag & MM_DBG_PRINT_SEED) {
fprintf(stderr, "RS\t%d\n", rep_len);
for (i = 0; i < n_a; ++i)
fprintf(stderr, "SD\t%s\t%d\t%c\t%d\t%d\t%d\n", mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
i == 0? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
}
timers[MM_TIME_SEED] += realtime() - t1;
t1 = realtime();
// set max chaining gap on the query and the reference sequence
if (is_sr)
max_chain_gap_qry = qlen_sum > opt->max_gap? qlen_sum : opt->max_gap;
else max_chain_gap_qry = opt->max_gap;
if (opt->max_gap_ref > 0) {
max_chain_gap_ref = opt->max_gap_ref; // always honor mm_mapopt_t::max_gap_ref if set
} else if (opt->max_frag_len > 0) {
max_chain_gap_ref = opt->max_frag_len - qlen_sum;
if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
} else max_chain_gap_ref = opt->max_gap;
chn_pen_gap = opt->chain_gap_scale * 0.01 * mi->k;
chn_pen_skip = opt->chain_skip_scale * 0.01 * mi->k;
if (opt->flag & MM_F_RMQ) {
a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
} else {
a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
if (opt->bw_long > opt->bw && (opt->flag & (MM_F_SPLICE|MM_F_SR|MM_F_NO_LJOIN)) == 0 && n_segs == 1 && n_regs0 > 1) { // re-chain/long-join for long sequences
int32_t st = (int32_t)a[0].y, en = (int32_t)a[(int32_t)u[0] - 1].y;
if (qlen_sum - (en - st) > opt->rmq_rescue_size || en - st > qlen_sum * opt->rmq_rescue_ratio) {
int32_t i;
for (i = 0, n_a = 0; i < n_regs0; ++i) n_a += (int32_t)u[i];
kfree(b->km, u);
radix_sort_128x(a, a + n_a);
a = mg_lchain_rmq(opt->max_gap, opt->rmq_inner_dist, opt->bw_long, opt->max_chain_skip, opt->rmq_size_cap, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, n_a, a, &n_regs0, &u, b->km);
}
} else if (opt->max_occ > opt->mid_occ && rep_len > 0 && !(opt->flag & MM_F_RMQ)) { // re-chain, mostly for short reads
int rechain = 0;
if (n_regs0 > 0) { // test if the best chain has all the segments
int n_chained_segs = 1, max = 0, max_i = -1, max_off = -1, off = 0;
for (i = 0; i < n_regs0; ++i) { // find the best chain
if (max < (int)(u[i]>>32)) max = u[i]>>32, max_i = i, max_off = off;
off += (uint32_t)u[i];
}
for (i = 1; i < (int32_t)u[max_i]; ++i) // count the number of segments in the best chain
if ((a[max_off+i].y&MM_SEED_SEG_MASK) != (a[max_off+i-1].y&MM_SEED_SEG_MASK))
++n_chained_segs;
if (n_chained_segs < n_segs)
rechain = 1;
} else rechain = 1;
if (rechain) { // redo chaining with a higher max_occ threshold
kfree(b->km, a);
kfree(b->km, u);
kfree(b->km, mini_pos);
if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else a = collect_seed_hits(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
a = mg_lchain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score,
chn_pen_gap, chn_pen_skip, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
}
b->frag_gap = max_chain_gap_ref;
b->rep_len = rep_len;
timers[MM_TIME_CHAIN] += realtime() - t1;
t1 = realtime();
regs0 = mm_gen_regs(b->km, hash, qlen_sum, n_regs0, u, a, !!(opt->flag&MM_F_QSTRAND));
if (mi->n_alt) {
mm_mark_alt(mi, n_regs0, regs0);
mm_hit_sort(b->km, &n_regs0, regs0, opt->alt_drop); // this step can be merged into mm_gen_regs(); will do if this shows up in profile
}
if (mm_dbg_flag & (MM_DBG_PRINT_SEED|MM_DBG_PRINT_CHAIN))
for (j = 0; j < n_regs0; ++j)
for (i = regs0[j].as; i < regs0[j].as + regs0[j].cnt; ++i)
fprintf(stderr, "CN\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", j, mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, "+-"[a[i].x>>63], (int32_t)a[i].y, (int32_t)(a[i].y>>32&0xff),
i == regs0[j].as? 0 : ((int32_t)a[i].y - (int32_t)a[i-1].y) - ((int32_t)a[i].x - (int32_t)a[i-1].x));
chain_post(opt, max_chain_gap_ref, mi, b->km, qlen_sum, n_segs, qlens, &n_regs0, regs0, a);
if (!is_sr && !(opt->flag&MM_F_QSTRAND)) {
mm_est_err(mi, qlen_sum, n_regs0, regs0, a, n_mini_pos, mini_pos);
n_regs0 = mm_filter_strand_retained(n_regs0, regs0);
}
if (n_segs == 1) { // uni-segment
regs0 = align_regs(opt, mi, b->km, qlens[0], seqs[0], &n_regs0, regs0, a);
regs0 = (mm_reg1_t*)realloc(regs0, sizeof(*regs0) * n_regs0);
mm_set_mapq(b->km, n_regs0, regs0, opt->min_chain_score, opt->a, rep_len, is_sr);
n_regs[0] = n_regs0, regs[0] = regs0;
} else { // multi-segment
mm_seg_t *seg;
seg = mm_seg_gen(b->km, hash, n_segs, qlens, n_regs0, regs0, n_regs, regs, a); // split fragment chain to separate segment chains
free(regs0);
for (i = 0; i < n_segs; ++i) {
mm_set_parent(b->km, opt->mask_level, opt->mask_len, n_regs[i], regs[i], opt->a * 2 + opt->b, opt->flag&MM_F_HARD_MLEVEL, opt->alt_drop); // update mm_reg1_t::parent
regs[i] = align_regs(opt, mi, b->km, qlens[i], seqs[i], &n_regs[i], regs[i], seg[i].a);
mm_set_mapq(b->km, n_regs[i], regs[i], opt->min_chain_score, opt->a, rep_len, is_sr);
}
mm_seg_free(b->km, n_segs, seg);
if (n_segs == 2 && opt->pe_ori >= 0 && (opt->flag&MM_F_CIGAR))
mm_pair(b->km, max_chain_gap_ref, opt->pe_bonus, opt->a * 2 + opt->b, opt->a, qlens, n_regs, regs); // pairing
}
timers[MM_TIME_ALIGN] += realtime() - t1;
kfree(b->km, mv.a);
kfree(b->km, a);
kfree(b->km, u);
kfree(b->km, mini_pos);
if (b->km) {
km_stat(b->km, &kmst);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "QM\t%s\t%d\tcap=%ld,nCore=%ld,largest=%ld\n", qname, qlen_sum, kmst.capacity, kmst.n_cores, kmst.largest);
assert(kmst.n_blocks == kmst.n_cores); // otherwise, there is a memory leak
if (kmst.largest > 1U<<28 || (opt->cap_kalloc > 0 && kmst.capacity > opt->cap_kalloc)) {
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "[W::%s] reset thread-local memory after read %s\n", __func__, qname);
km_destroy(b->km);
b->km = km_init();
}
}
}
mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
mm_reg1_t *regs;
mm_map_frag(mi, 1, &qlen, &seq, n_regs, ®s, b, opt, qname);
return regs;
}
/**************************
* Multi-threaded mapping *
**************************/
typedef struct {
int n_processed, n_threads, n_fp;
int64_t mini_batch_size;
const mm_mapopt_t *opt;
mm_bseq_file_t **fp;
const mm_idx_t *mi;
kstring_t str;
int n_parts;
uint32_t *rid_shift;
FILE *fp_split, **fp_parts;
} pipeline_t;
typedef struct {
const pipeline_t *p;
int n_seq, n_frag;
mm_bseq1_t *seq;
int *n_reg, *seg_off, *n_seg, *rep_len, *frag_gap;
mm_reg1_t **reg;
mm_tbuf_t **buf;
#if defined(__AMD_SPLIT_KERNELS__)
mm_trbuf_t **trbuf;
int batch_max_reads;
size_t batch_max_anchors;
int gpu_min_n;
#endif
} step_t;
#define MIN(a, b) ((a)<(b)?(a):(b))
#define MAX(a, b) ((a)>(b)?(a):(b))
// consolidate timers from worker threads
void mm_consolidate_timers(step_t *s, pipeline_t *p)
{
// TODO: disabled for sysbio submission
return;
mm_time_seed_min = 0;
mm_time_chain_min = 0;
mm_time_align_min = 0;
mm_time_seed_max = 0;
mm_time_chain_max = 0;
mm_time_align_max = 0;
mm_time_seed_avg = 0;
mm_time_chain_avg = 0;
mm_time_align_avg = 0;
for (int i = 0; i < p->n_threads; ++i) {
mm_time_seed_min = MIN(mm_time_seed_min, s->buf[i]->timers[MM_TIME_SEED]);
mm_time_chain_min = MIN(mm_time_chain_min, s->buf[i]->timers[MM_TIME_CHAIN]);
mm_time_align_min = MIN(mm_time_align_min, s->buf[i]->timers[MM_TIME_ALIGN]);
mm_time_seed_max = MAX(mm_time_seed_max, s->buf[i]->timers[MM_TIME_SEED]);
mm_time_chain_max = MAX(mm_time_chain_max, s->buf[i]->timers[MM_TIME_CHAIN]);
mm_time_align_max = MAX(mm_time_align_max, s->buf[i]->timers[MM_TIME_ALIGN]);
mm_time_seed_avg += s->buf[i]->timers[MM_TIME_SEED];
mm_time_chain_avg += s->buf[i]->timers[MM_TIME_CHAIN];
mm_time_align_avg += s->buf[i]->timers[MM_TIME_ALIGN];
mm_time_seed_sum += s->buf[i]->timers[MM_TIME_SEED];
mm_time_chain_sum += s->buf[i]->timers[MM_TIME_CHAIN];
mm_time_align_sum += s->buf[i]->timers[MM_TIME_ALIGN];
}
mm_time_seed_avg /= p->n_threads;
mm_time_chain_avg /= p->n_threads;
mm_time_align_avg /= p->n_threads;
fprintf(stderr, "----------------------------------------------------\n");
fprintf(stderr, " Min (sec) Max (sec) Avg (sec) \n");
fprintf(stderr, "----------------------------------------------------\n");
fprintf(stderr, "Seed = %11.3f %11.3f %11.3f\n",
mm_time_seed_min, mm_time_seed_max, mm_time_seed_avg);
fprintf(stderr, "Chain = %11.3f %11.3f %11.3f\n",
mm_time_chain_min, mm_time_chain_max, mm_time_chain_avg);
fprintf(stderr, "Align = %11.3f %11.3f %11.3f\n",
mm_time_align_min, mm_time_align_max, mm_time_align_avg);
fprintf(stderr, "----------------------------------------------------\n");
fprintf(stderr, "Avg (seed + chain + align) per thread = %.3f secs\n", (mm_time_seed_avg + mm_time_chain_avg + mm_time_align_avg));
fprintf(stderr, "Total (seed + chain + align) (all batches) for %d thread(s) = %.3f secs\n", p->n_threads, (mm_time_seed_sum + mm_time_chain_sum + mm_time_align_sum));
}
#if defined(__AMD_SPLIT_KERNELS__)
void mm_trbuf_is_full(mm_trbuf_t* tr, step_t *s){
while (tr->acc_batch.total_n > s->batch_max_anchors) { // if the batch is full
tr->is_full = 1;
tr->is_pending = 1;
// move last read from acc_batch to pending batch (another memory poll)
chain_read_t *read_ptr_acc_batch = &tr->acc_batch.reads[tr->acc_batch.count - 1];
chain_read_t *read_ptr_pending_batch = &tr->pending_batch.reads[tr->pending_batch.count];
/* deep copy, with memory pool transaction*/
*read_ptr_pending_batch = *read_ptr_acc_batch;
if (s->p->opt->flag & MM_F_INDEPEND_SEG) {
read_ptr_pending_batch->qlens = (int *)kmalloc(tr->pending_batch.km, sizeof(int));
read_ptr_pending_batch->qseqs = (const char **)kmalloc(tr->pending_batch.km, sizeof(const char*));
read_ptr_pending_batch->qlens[0] = read_ptr_acc_batch->qlens[0];
read_ptr_pending_batch->qseqs[0] = read_ptr_acc_batch->qseqs[0];
} else {
read_ptr_pending_batch->qlens = (int *)kmalloc(tr->pending_batch.km, sizeof(int)*read_ptr_acc_batch->n_seg);
read_ptr_pending_batch->qseqs = (const char **)kmalloc(tr->pending_batch.km, sizeof(const char*)*read_ptr_acc_batch->n_seg);
memcpy(read_ptr_pending_batch->qlens, read_ptr_acc_batch->qlens, sizeof(int)*read_ptr_acc_batch->n_seg);
memcpy(read_ptr_pending_batch->qseqs, read_ptr_acc_batch->qseqs, sizeof(const char*)*read_ptr_acc_batch->n_seg);
}
read_ptr_pending_batch->mini_pos = (uint64_t*)kmalloc(tr->pending_batch.km, read_ptr_acc_batch->n_mini_pos * sizeof(uint64_t));
read_ptr_pending_batch->a = (mm128_t*)kmalloc(tr->pending_batch.km, read_ptr_acc_batch->n * sizeof(mm128_t));
memcpy(read_ptr_pending_batch->mini_pos, read_ptr_acc_batch->mini_pos, read_ptr_acc_batch->n_mini_pos * sizeof(uint64_t));
memcpy(read_ptr_pending_batch->a, read_ptr_acc_batch->a, read_ptr_acc_batch->n * sizeof(mm128_t));
strcpy(read_ptr_pending_batch->seq.name, read_ptr_acc_batch->seq.name);
tr->pending_batch.count++;
tr->pending_batch.total_n += read_ptr_acc_batch->n;
// remove read from acc_batch
tr->acc_batch.count--;
tr->acc_batch.total_n -= read_ptr_acc_batch->n;
kfree(tr->acc_batch.km, read_ptr_acc_batch->mini_pos);
kfree(tr->acc_batch.km, read_ptr_acc_batch->a);
kfree(tr->acc_batch.km, read_ptr_acc_batch->qlens);
kfree(tr->acc_batch.km, read_ptr_acc_batch->qseqs);
}
}
static void worker_for(void *_data, long i_in, int tid) // kt_for() callback
{
step_t *s = (step_t *)_data;
long i = i_in;
int j, iread, off, pe_ori = s->p->opt->pe_ori;
double t = 0.0;
mm_tbuf_t *b = s->buf[tid];
mm_trbuf_t *tr = s->trbuf[tid];
// Check if this is a valid read
if (i != -1) {
off = s->seg_off[i];
assert(s->n_seg[i] <= MM_MAX_SEG);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME) {
fprintf(stderr, "QR\t%s\t%d\t%d\n", s->seq[off].name, tid, s->seq[off].l_seq);
t = realtime();
}
int n_indep_reads = (s->p->opt->flag & MM_F_INDEPEND_SEG) ? s->n_seg[i] : 1;
void *km;
chain_read_t *read_ptr = 0;
if ( n_indep_reads + tr->acc_batch.count <= s->batch_max_reads){
read_ptr = tr->acc_batch.reads + tr->acc_batch.count;
tr->acc_batch.count += n_indep_reads;
km = tr->acc_batch.km;
} else {
read_ptr = tr->pending_batch.reads + tr->pending_batch.count;
tr->pending_batch.count += n_indep_reads;
tr->is_full = 1;
tr->is_pending = 1;
km = tr->pending_batch.km;
}
if (s->p->opt->flag & MM_F_INDEPEND_SEG) { // assign to different chain_read_t if segments are indepent
for (j = 0; j < s->n_seg[i]; ++j) {
read_ptr->qlens = (int *)kmalloc(km, sizeof(int));
read_ptr->qseqs = (const char **)kmalloc(km, sizeof(const char *));
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
mm_revcomp_bseq(&s->seq[off + j]);
read_ptr->qlens[0] = s->seq[off + j].l_seq;
read_ptr->qseqs[0] = s->seq[off + j].seq;
read_ptr->n_seg = 1;
read_ptr->seq.i = i;
read_ptr->seq.seg_id = j;
strcpy(read_ptr->seq.name, s->seq[off + j].name);
read_ptr->seq.n_alt = s->p->mi->n_alt;
read_ptr->seq.is_alt = 0;
read_ptr++;
}
} else {
read_ptr->qlens = (int *)kmalloc(km, s->n_seg[i] * sizeof(int));
read_ptr->qseqs = (const char **)kmalloc(km, s->n_seg[i] * sizeof(const char *));
read_ptr->n_seg = s->n_seg[i];
for (j = 0; j < s->n_seg[i]; ++j) {
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
mm_revcomp_bseq(&s->seq[off + j]);
read_ptr->qlens[j] = s->seq[off + j].l_seq;
read_ptr->qseqs[j] = s->seq[off + j].seq;
}
read_ptr->seq.i = i;
read_ptr->seq.seg_id = 0;
strcpy(read_ptr->seq.name, s->seq[off].name);
read_ptr->seq.n_alt = s->p->mi->n_alt;
read_ptr->seq.is_alt = 0;
read_ptr++;
}
// Seed
for (j = 0; j < n_indep_reads; j++) {
read_ptr--;