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Purge_Dups.cpp
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#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include <stdlib.h>
#include "ksort.h"
#include "Purge_Dups.h"
#include "Overlaps.h"
#include "Correct.h"
#include "kthread.h"
#include "kdq.h"
KDQ_INIT(uint64_t)
#define Cal_Off(OFF) ((long long)((uint32_t)((OFF)>>32)) - (long long)((uint32_t)((OFF))))
#define Get_xOff(OFF) ((long long)((uint32_t)((OFF)>>32)))
#define Get_yOff(OFF) ((long long)((uint32_t)((OFF))))
#define Get_match(x) ((x).weight)
#define Get_total(x) ((x).index_beg)
#define Get_type(x) ((x).index_end)
#define Get_x_beg(x) ((x).x_beg_pos)
#define Get_x_end(x) ((x).x_end_pos)
#define Get_y_beg(x) ((x).y_beg_pos)
#define Get_y_end(x) ((x).y_end_pos)
#define Get_rev(x) ((x).rev)
uint8_t debug_enable = 0;
typedef struct {
asg_arc_t x;
uint64_t Off;
uint64_t weight;
}asg_arc_t_offset;
typedef struct {
kvec_t(asg_arc_t_offset) a;
uint64_t i;
}kvec_asg_arc_t_offset;
typedef struct {
uint64_t weight;
uint32_t x_beg_pos;
uint32_t x_end_pos;
uint32_t y_beg_pos;
uint32_t y_end_pos;
uint32_t index_beg;
uint32_t index_end;
uint8_t rev;
asg_arc_t t;
}hap_candidates;
typedef struct {
kvec_t(hap_candidates) a;
uint64_t i;
}kvec_hap_candidates;
#define SELF_EXIST 0
#define REVE_EXIST 1
#define DELETE 2
typedef struct {
uint8_t rev;
uint8_t type;
uint8_t status;
uint32_t x_beg_pos;
uint32_t x_end_pos;
uint32_t y_beg_pos;
uint32_t y_end_pos;
uint32_t x_beg_id;
uint32_t x_end_id;
uint32_t y_beg_id;
uint32_t y_end_id;
uint32_t xUid;
uint32_t yUid;
uint32_t weight;
}hap_overlaps;
typedef struct {
kvec_t(hap_overlaps) a;
}kvec_hap_overlaps;
typedef struct {
kvec_hap_overlaps* x;
uint32_t num;
}hap_overlaps_list;
typedef struct {
uint64_t* vote_counting;
uint8_t* visit;
kvec_t_u64_warp u_vecs;
kvec_asg_arc_t_offset u_buffer;
kvec_t_i32_warp u_buffer_tailIndex;
kvec_t_i32_warp u_buffer_prevIndex;
kvec_t_u8_warp u_buffer_flag;
kvec_t_i32_warp u_buffer_beg;
kvec_hap_candidates u_can;
}hap_alignment_struct;
typedef struct {
hap_alignment_struct* buf;
uint32_t num_threads;
ma_ug_t *ug;
asg_t *read_g;
ma_hit_t_alloc* sources;
ma_hit_t_alloc* reverse_sources;
R_to_U* ruIndex;
ma_sub_t *coverage_cut;
uint64_t* position_index;
float Hap_rate;
int max_hang;
int min_ovlp;
float chain_rate;
hap_overlaps_list* all_ovlp;
long long cov_threshold;
}hap_alignment_struct_pip;
void print_peak_line(int c, int x, int exceed, int64_t cnt)
{
int j;
if (c >= 0) fprintf(stderr, "[M::%s] %5d: ", __func__, c);
else fprintf(stderr, "[M::%s] %5s: ", __func__, "rest");
for (j = 0; j < x; ++j) fputc('*', stderr);
if (exceed) fputc('>', stderr);
fprintf(stderr, " %lld\n", (long long)cnt);
}
void print_peak(long long* cov_buf, long long cov_buf_length, long long max_i)
{
long long i;
const long long hist_max = 100;
// print histogram
for (i = 0; i < cov_buf_length; ++i)
{
long long x, exceed = 0;
x = (int)((double)hist_max * cov_buf[i] / cov_buf[max_i] + .499);
if (x > hist_max) exceed = 1, x = hist_max; // may happen if cnt[2] is higher
if (i > max_i && x == 0) break;
print_peak_line(i, x, exceed, cov_buf[i]);
}
{
long long x, exceed = 0;
long long rest = 0;
for (; i < cov_buf_length; ++i) rest += cov_buf[i];
x = (int)((double)hist_max * rest / cov_buf[max_i] + .499);
if (x > hist_max) exceed = 1, x = hist_max;
print_peak_line(-1, x, exceed, rest);
}
}
void get_read_peak(long long* cov_buf, long long cov_buf_length, long long* topo_peak_cov,
long long* hom_peak, long long* het_peak, long long* k_mer_only, long long* coverage_only)
{
long long i, start, err_i, max_i, max2_i, max3_i, topo_peak_i, max, max2, max3, topo_peak, min;
i = start = err_i = max_i = max2_i = max3_i = topo_peak_i = -1;
max = max2 = max3 = topo_peak = min = -1;
///cov_buf[0] is usually very large
for (i = 1; i < cov_buf_length; ++i)
{
if(cov_buf[i] > cov_buf[i-1]) break;
}
err_i = i - 1;
// find the global highest peak
max_i = err_i + 1, max = cov_buf[max_i];
for (i = max_i; i < cov_buf_length; ++i)
{
if (cov_buf[i] > max)
{
max = cov_buf[i];
max_i = i;
}
}
///print_peak(cov_buf, cov_buf_length, max_i);
// look for smaller peak on the low end
max2 = -1; max2_i = -1;
for (i = max_i - 1; i > err_i; --i)
{
///at first, it should be a peak
if (cov_buf[i] >= cov_buf[i-1] && cov_buf[i] >= cov_buf[i+1])
{
if (cov_buf[i] > max2)
{
max2 = cov_buf[i];
max2_i = i;
}
}
}
///fprintf(stderr, "***max2: %lld, max2_i: %lld\n", max2, max2_i);
if (max2_i != -1 && max2_i > err_i && max2_i < max_i)
{
for (i = max2_i + 1, min = max; i < max_i; ++i)
{
if (cov_buf[i] < min) min = cov_buf[i];
}
///if the second peak is not significant
if(max2 < max * 0.05 || min > max2 * 0.95) max2 = max2_i = -1;
}
// look for smaller peak on the high end
max3 = -1; max3_i = -1;
// we'd better use i < cov_buf_length - 1, since cov_buf[cov_buf_length-1] may have problem
for (i = max_i + 1; i < cov_buf_length - 1; ++i)
{
//at first, it should be a peak
if (cov_buf[i] >= cov_buf[i-1] && cov_buf[i] >= cov_buf[i+1])
{
if (cov_buf[i] > max3)
{
max3 = cov_buf[i], max3_i = i;
}
}
}
///fprintf(stderr, "***max3: %lld, max3_i: %lld\n", max3, max3_i);
//if found a peak
if (max3 != -1 && max3_i > max_i)
{
for (i = max_i + 1, min = max; i < max3_i; ++i)
{
if (cov_buf[i] < min) min = cov_buf[i];
}
if (max3 < max * 0.05 || min > max3 * 0.95 || max3_i > max_i * 3) max3 = max3_i = -1;
}
(*hom_peak) = (*het_peak) = -1;
if (topo_peak_cov && (*topo_peak_cov) < cov_buf_length)
{
topo_peak_i = (*topo_peak_cov);
topo_peak = cov_buf[topo_peak_i];
if (topo_peak <= max * 0.05) topo_peak_i = topo_peak = -1;
}
long long k_mer_het, k_mer_hom, coverage_het, coverage_hom, alter_peak;
k_mer_het = k_mer_hom = coverage_het = coverage_hom = alter_peak = -1;
alter_peak = topo_peak_i;
k_mer_het = asm_opt.het_cov;
k_mer_hom = asm_opt.hom_cov;
if(max3_i > 0)
{
coverage_het = max_i;
coverage_hom = max3_i;
}
else
{
coverage_het = max2_i;
coverage_hom = max_i;
}
if(k_mer_het != -1)
{
(*het_peak) = k_mer_het;
(*hom_peak) = k_mer_hom;
return;
}
else if(coverage_het != -1)
{
(*het_peak) = coverage_het;
(*hom_peak) = coverage_hom;
return;
}
else if(k_mer_hom > coverage_hom*1.5)
{
(*het_peak) = coverage_hom;
(*hom_peak) = k_mer_hom;
return;
}
else if(alter_peak != -1)
{
///if peak is het, coverage peak is more reliable
if(coverage_hom >= alter_peak*0.8 && coverage_hom <= alter_peak*1.2)
{
(*het_peak) = coverage_hom;
return;
}///if peak is homo, k-mer peak is more reliable
else if(k_mer_hom >= alter_peak*0.8*2 && k_mer_hom <= alter_peak*1.2*2)
{
(*hom_peak) = k_mer_hom;
return;
}
}
(*k_mer_only) = k_mer_hom;
(*coverage_only) = coverage_hom;
// fprintf(stderr, "max: %lld, max_i: %lld\n", max, max_i);
// fprintf(stderr, "max2: %lld, max2_i: %lld\n", max2, max2_i);
// fprintf(stderr, "max3: %lld, max3_i: %lld\n", max3, max3_i);
// fprintf(stderr, "[M::%s] Heterozygous k-mer peak: %d\n", __func__, asm_opt.het_cov);
// fprintf(stderr, "[M::%s] Homozygous k-mer peak: %d\n", __func__, asm_opt.hom_cov);
// fprintf(stderr, "[M::%s] Heterozygous coverage peak: %lld\n", __func__, (*het_peak));
// fprintf(stderr, "[M::%s] Homozygous coverage peak: %lld\n", __func__, (*hom_peak));
// fprintf(stderr, "[M::%s] Alter coverage peak: %lld\n", __func__, topo_peak_i);
}
long long get_alter_peak(ma_ug_t *ug, asg_t *read_g, R_to_U* ruIndex, uint64_t* position_index,
ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, long long cov_buf_length)
{
ma_utg_t* u = NULL;
asg_t* nsg = ug->g;
uint64_t v, j, k, qn, n_vtx = nsg->n_seq, primary_bases = 0, alter_bases = 0;
uint32_t tn, is_Unitig;
long long* cov_buf = NULL;
ma_hit_t *h;
cov_buf = (long long*)calloc(cov_buf_length, sizeof(long long));
long long R_bases = 0, C_bases_primary = 0, C_bases_alter = 0, C_bases = 0;
memset(position_index, -1, sizeof(uint64_t)*read_g->n_seq);
for (v = 0; v < n_vtx; ++v)
{
if(nsg->seq[v].del) continue;
if(nsg->seq[v].c == ALTER_LABLE) continue;
u = &(ug->u.a[v]);
if(u->m == 0) continue;
for (k = 0; k < u->n; k++)
{
qn = u->a[k]>>33;
position_index[qn] = 0;
R_bases = coverage_cut[qn].e - coverage_cut[qn].s;
primary_bases += R_bases;
}
}
for (qn = 0; qn < read_g->n_seq; qn++)
{
if(position_index[qn] == 0) continue;
if(read_g->seq[qn].del) continue;
C_bases = C_bases_primary = C_bases_alter = 0;
R_bases = coverage_cut[qn].e - coverage_cut[qn].s;
alter_bases += R_bases;
for (j = 0; j < (uint64_t)(sources[qn].length); j++)
{
h = &(sources[qn].buffer[j]);
if(h->el != 1) continue;
tn = Get_tn((*h));
if(read_g->seq[tn].del == 1)
{
///get the id of read that contains it
get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
}
if(position_index[tn] == 0)
{
C_bases_primary += Get_qe((*h)) - Get_qs((*h));
}
else
{
C_bases_alter += Get_qe((*h)) - Get_qs((*h));
}
}
// if(qn == 1893151 || qn == 1929038)
// {
// fprintf(stderr, "qn: %lu, C_bases_primary: %lld, C_bases_alter: %lld, C_bases: %lld\n",
// qn, C_bases_primary, C_bases_alter, C_bases);
// }
C_bases = C_bases_primary + C_bases_alter;
if(C_bases_alter < C_bases * ALTER_COV_THRES) continue;
C_bases = C_bases/R_bases;
if(C_bases < 0 || C_bases >= cov_buf_length) continue;
cov_buf[C_bases]++;
}
long long max_i = -1, max = -1;
for (j = 0; (long long)j < cov_buf_length; ++j)
{
if (cov_buf[j] > max)
{
max = cov_buf[j];
max_i = j;
}
}
///fprintf(stderr, "alter max_i: %lld, max: %lld\n", max_i, max);
///if(max_i < 5) max_i = max = -1;
if(alter_bases < primary_bases * REAL_ALTER_THRES) max_i = max = -1;
free(cov_buf);
memset(position_index, -1, sizeof(uint64_t)*read_g->n_seq);
return max_i;
}
long long get_read_coverage_thres(ma_ug_t *ug, asg_t *read_g, R_to_U* ruIndex, uint64_t* position_index,
ma_hit_t_alloc* sources, ma_sub_t* coverage_cut, uint64_t n_read, long long cov_buf_length,
long long* k_mer_only, long long* coverage_only)
{
uint64_t i, j;
long long* cov_buf = NULL;
ma_hit_t *h;
cov_buf = (long long*)calloc(cov_buf_length, sizeof(long long));
long long R_bases = 0, C_bases = 0;
for (i = 0; i < n_read; ++i)
{
C_bases = 0;
R_bases = coverage_cut[i].e - coverage_cut[i].s;
for (j = 0; j < (uint64_t)(sources[i].length); j++)
{
h = &(sources[i].buffer[j]);
if(h->el != 1) continue;
C_bases += Get_qe((*h)) - Get_qs((*h));
}
C_bases = C_bases/R_bases;
if(C_bases < 0 || C_bases >= cov_buf_length) continue;
cov_buf[C_bases]++;
}
long long alter_peak = -1, hom_peak = -1, het_peak = -1;
if(position_index)
{
alter_peak = get_alter_peak(ug, read_g, ruIndex, position_index, sources, coverage_cut,
cov_buf_length);
}
get_read_peak(cov_buf, cov_buf_length, alter_peak == -1? NULL: &alter_peak, &hom_peak, &het_peak,
k_mer_only, coverage_only);
free(cov_buf);
if(hom_peak != -1) return hom_peak*HOM_PEAK_RATE;
if(het_peak != -1) return het_peak*HET_PEAK_RATE;
return -1;
}
void init_hap_alignment_struct(hap_alignment_struct* x, uint32_t size)
{
x->vote_counting = (uint64_t*)malloc(sizeof(uint64_t)*size);
memset(x->vote_counting, 0, sizeof(uint64_t)*size);
x->visit = (uint8_t*)malloc(sizeof(uint8_t)*size);
memset(x->visit, 0, size);
kv_init(x->u_vecs.a);
kv_init(x->u_buffer.a);
kv_init(x->u_buffer_tailIndex.a);
kv_init(x->u_buffer_prevIndex.a);
kv_init(x->u_buffer_beg.a);
kv_init(x->u_buffer_flag.a);
kv_init(x->u_can.a);
}
void destory_hap_alignment_struct(hap_alignment_struct* x)
{
free(x->vote_counting);
free(x->visit);
kv_destroy(x->u_vecs.a);
kv_destroy(x->u_buffer.a);
kv_destroy(x->u_buffer_tailIndex.a);
kv_destroy(x->u_buffer_prevIndex.a);
kv_destroy(x->u_buffer_beg.a);
kv_destroy(x->u_buffer_flag.a);
kv_destroy(x->u_can.a);
}
void init_hap_alignment_struct_pip(hap_alignment_struct_pip* x, uint32_t num_threads, uint32_t n_seq,
ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, ma_sub_t *coverage_cut,
uint64_t* position_index, float Hap_rate, int max_hang, int min_ovlp, float chain_rate, hap_overlaps_list* all_ovlp)
{
uint32_t i;
x->num_threads = num_threads;
x->buf = (hap_alignment_struct*)malloc(sizeof(hap_alignment_struct)*x->num_threads);
for (i = 0; i < x->num_threads; i++)
{
init_hap_alignment_struct(&(x->buf[i]), n_seq);
}
x->ug = ug;
x->read_g = read_g;
x->sources = sources;
x->reverse_sources = reverse_sources;
x->ruIndex = ruIndex;
x->coverage_cut = coverage_cut;
x->position_index = position_index;
x->Hap_rate = Hap_rate;
x->max_hang = max_hang;
x->min_ovlp = min_ovlp;
x->chain_rate = chain_rate;
x->all_ovlp = all_ovlp;
}
void destory_hap_alignment_struct_pip(hap_alignment_struct_pip* x)
{
uint32_t i;
for (i = 0; i < x->num_threads; i++)
{
destory_hap_alignment_struct(&(x->buf[i]));
}
free(x->buf);
}
void init_hap_overlaps_list(hap_overlaps_list* x, uint32_t num)
{
uint32_t i = 0;
x->num = num;
x->x = (kvec_hap_overlaps*)malloc(sizeof(kvec_hap_overlaps)*x->num);
for (i = 0; i < x->num; i++)
{
kv_init(x->x[i].a);
}
}
void enable_debug_mode(uint32_t mode)
{
debug_enable = mode;
}
void destory_hap_overlaps_list(hap_overlaps_list* x)
{
uint32_t i = 0;
for (i = 0; i < x->num; i++)
{
kv_destroy(x->x[i].a);
}
free(x->x);
}
inline void clean_visit_flag(uint8_t* visit, asg_t *read_g, R_to_U* ruIndex, uint32_t contigNum,
ma_hit_t_alloc* x)
{
uint32_t k, rId, is_Unitig, Hap_cId;
if(x->length*2 > contigNum)
{
memset(visit, 0, contigNum);
}
else
{
for (k = 0; k < x->length; k++)
{
rId = Get_tn(x->buffer[k]);
if(read_g->seq[rId].del == 1)
{
///get the id of read that contains it
get_R_to_U(ruIndex, rId, &rId, &is_Unitig);
if(rId == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[rId].del == 1) continue;
}
///there are two cases:
///1. read at primary contigs, get_R_to_U() return its corresponding contig Id
///2. read at alternative contigs, get_R_to_U() return (uint32_t)-1
get_R_to_U(ruIndex, rId, &Hap_cId, &is_Unitig);
if(is_Unitig == 0 || Hap_cId == (uint32_t)-1) continue;
///here rId is the id of the read coming from the different haplotype
///Hap_cId is the id of the corresponding contig (note here is the contig, instead of untig)
visit[Hap_cId] = 0;
}
}
}
uint32_t prefilter(uint32_t x_pos, uint32_t y_pos, uint32_t xLen, uint32_t yLen, uint32_t dir,
float Hap_rate, uint32_t seedOcc)
{
uint32_t max_count = 0, min_count = 0;
uint32_t /**xLeftBeg, **/xLeftLen, yLeftBeg, yLeftLen;
uint32_t xRightBeg, xRightLen, yRightBeg, yRightLen;
if(dir == 0)
{
/**xLeftBeg = 0;**/ xLeftLen = x_pos; xRightBeg = x_pos; xRightLen = xLen - xRightBeg;
yLeftBeg = 0; yLeftLen = y_pos; yRightBeg = y_pos; yRightLen = yLen - yRightBeg;
}
else
{
/**xLeftBeg = 0;**/ xLeftLen = x_pos; xRightBeg = x_pos; xRightLen = xLen - xRightBeg;
yLeftBeg = y_pos + 1; yLeftLen = yLen - yLeftBeg;
yRightBeg = 0; yRightLen = y_pos + 1;
}
max_count = seedOcc;
min_count = MIN(xLeftLen, yLeftLen) + MIN(xRightLen, yRightLen);
if(min_count == 0) return NON_PLOID;
if(max_count <= min_count*Hap_rate) return NON_PLOID;
return PLOID;
}
inline uint64_t get_xy_pos(asg_t *read_g, asg_arc_t* t, uint32_t v_in_unitig, uint32_t w_in_unitig,
uint32_t xUnitigLen, uint32_t yUnitigLen, uint64_t* position_index, uint8_t* rev)
{
uint32_t x_pos, y_pos, x_dir = 0, y_dir = 0;
uint64_t tmp;
x_pos = y_pos = (uint32_t)-1;
if((t->ul>>32)==v_in_unitig)///end pos
{
x_pos = (position_index[v_in_unitig>>1]>>32) + read_g->seq[v_in_unitig>>1].len - 1;
x_dir = 0;
}
else if((t->ul>>32)==(v_in_unitig^1))///start pos
{
x_pos = (position_index[v_in_unitig>>1]>>32);
x_dir = 1;
}
else
{
fprintf(stderr, "ERROR\n");
}
if(t->v == w_in_unitig)
{
y_pos = (position_index[w_in_unitig>>1]>>32) + t->ol - 1;
y_dir = 0;
}
else if(t->v == (w_in_unitig^1))
{
y_pos = (position_index[w_in_unitig>>1]>>32) + read_g->seq[w_in_unitig>>1].len - t->ol;
y_dir = 1;
}
else
{
fprintf(stderr, "ERROR\n");
}
(*rev) = x_dir^y_dir;
if((*rev))
{
if(yUnitigLen <= y_pos)
{
y_pos = (uint32_t)-1;
}
else
{
y_pos = yUnitigLen - y_pos - 1;
}
}
if(x_pos>=xUnitigLen) x_pos = (uint32_t)-1;
if(y_pos>=yUnitigLen) y_pos = (uint32_t)-1;
tmp = x_pos; tmp = tmp << 32; tmp = tmp | y_pos;
return tmp;
}
void print_debug_unitig(ma_utg_t *xReads, uint64_t* position_index, const char* infor)
{
uint32_t k;
fprintf(stderr, "\n%s: n = %u\n", infor, xReads->n);
for (k = 0; k < xReads->n; k++)
{
fprintf(stderr, "(%u)v: %u, len: %u, index: %u, pos: %u\n",
k, (uint32_t)(xReads->a[k]>>32), (uint32_t)xReads->a[k], (uint32_t)(position_index[xReads->a[k]>>33]),
(uint32_t)(position_index[xReads->a[k]>>33]>>32));
}
}
void deduplicate_edge(kvec_asg_arc_t_offset* u_buffer)
{
if(u_buffer->a.n == 0) return;
long long i = u_buffer->a.n - 1, k, i_off;
uint32_t v = u_buffer->a.a[i].x.ul>>33, m;
for (; i >= 0; i--)
{
if((u_buffer->a.a[i].x.ul>>33) != v)
{
break;
}
}
///fprintf(stderr, "u_buffer->a.n: %u, i: %lld\n", u_buffer->a.n, i);
i = i + 1;
for (m = i; i < (long long)u_buffer->a.n; i++)
{
if(u_buffer->a.a[i].x.del) continue;
i_off = Cal_Off(u_buffer->a.a[i].Off);
for (k = i + 1; k < (long long)u_buffer->a.n; k++)
{
if(u_buffer->a.a[k].x.del) continue;
if(u_buffer->a.a[i].x.el != u_buffer->a.a[k].x.el) continue;
if(i_off != Cal_Off(u_buffer->a.a[k].Off)) continue;
u_buffer->a.a[k].x.del = 1;
u_buffer->a.a[i].weight += u_buffer->a.a[k].weight;
}
u_buffer->a.a[m] = u_buffer->a.a[i];
m++;
}
u_buffer->a.n = m;
///fprintf(stderr, "u_buffer->a.n: %u, i: %lld\n", u_buffer->a.n, i);
}
int cmp_hap_alignment(const void * a, const void * b)
{
if((*(asg_arc_t_offset*)a).x.el > (*(asg_arc_t_offset*)b).x.el) return 1;
if((*(asg_arc_t_offset*)a).x.el < (*(asg_arc_t_offset*)b).x.el) return -1;
long long aOff = Cal_Off((*(asg_arc_t_offset*)a).Off);
long long bOff = Cal_Off((*(asg_arc_t_offset*)b).Off);
if(aOff > bOff) return 1;
if(aOff < bOff) return -1;
if(((*(asg_arc_t_offset*)a).Off>>32) > ((*(asg_arc_t_offset*)b).Off>>32)) return 1;
if(((*(asg_arc_t_offset*)a).Off>>32) < ((*(asg_arc_t_offset*)b).Off>>32)) return -1;
if((uint32_t)((*(asg_arc_t_offset*)a).Off) > (uint32_t)((*(asg_arc_t_offset*)b).Off)) return 1;
if((uint32_t)((*(asg_arc_t_offset*)a).Off) < (uint32_t)((*(asg_arc_t_offset*)b).Off)) return -1;
if((*(asg_arc_t_offset*)a).weight < (*(asg_arc_t_offset*)b).weight) return 1;
if((*(asg_arc_t_offset*)a).weight > (*(asg_arc_t_offset*)b).weight) return -1;
return 0;
}
int cmp_hap_alignment_chaining(const void * a, const void * b)
{
if((*(asg_arc_t_offset*)a).x.el > (*(asg_arc_t_offset*)b).x.el) return 1;
if((*(asg_arc_t_offset*)a).x.el < (*(asg_arc_t_offset*)b).x.el) return -1;
if(((*(asg_arc_t_offset*)a).Off>>32) > ((*(asg_arc_t_offset*)b).Off>>32)) return 1;
if(((*(asg_arc_t_offset*)a).Off>>32) < ((*(asg_arc_t_offset*)b).Off>>32)) return -1;
if((uint32_t)((*(asg_arc_t_offset*)a).Off) > (uint32_t)((*(asg_arc_t_offset*)b).Off)) return 1;
if((uint32_t)((*(asg_arc_t_offset*)a).Off) < (uint32_t)((*(asg_arc_t_offset*)b).Off)) return -1;
return 0;
}
int cmp_hap_candidates(const void * a, const void * b)
{
if((*(hap_candidates*)a).weight < (*(hap_candidates*)b).weight) return 1;
if((*(hap_candidates*)a).weight > (*(hap_candidates*)b).weight) return -1;
if((*(hap_candidates*)a).index_beg > (*(hap_candidates*)b).index_beg) return 1;
if((*(hap_candidates*)a).index_beg < (*(hap_candidates*)b).index_beg) return -1;
return 0;
}
inline long long get_hap_overlapLen(long long x_beg, long long x_end, long long xLen,
long long y_beg, long long y_end, long long yLen, long long* n_x_beg, long long* n_x_end,
long long* n_y_beg, long long* n_y_end)
{
if(x_beg <= y_beg)
{
y_beg = y_beg - x_beg;
x_beg = 0;
}
else
{
x_beg = x_beg - y_beg;
y_beg = 0;
}
long long x_right_length = xLen - x_end - 1;
long long y_right_length = yLen - y_end - 1;
if(x_right_length <= y_right_length)
{
x_end = xLen - 1;
y_end = y_end + x_right_length;
}
else
{
x_end = x_end + y_right_length;
y_end = yLen - 1;
}
if(n_x_beg) (*n_x_beg) = x_beg;
if(n_x_end) (*n_x_end) = x_end;
if(n_y_beg) (*n_y_beg) = y_beg;
if(n_y_end) (*n_y_end) = y_end;
return x_end - x_beg + 1;
}
#define X2Y 0
#define Y2X 1
#define XCY 2
#define YCX 3
uint32_t classify_hap_overlap(long long xBeg, long long xEnd, long long xLen,
long long yBeg, long long yEnd, long long yLen, long long* r_xBeg, long long* r_xEnd,
long long* r_yBeg, long long* r_yEnd)
{
long long n_x_beg, n_x_end, n_y_beg, n_y_end;
get_hap_overlapLen(xBeg, xEnd, xLen, yBeg, yEnd, yLen, &n_x_beg, &n_x_end, &n_y_beg, &n_y_end);
if(r_xBeg) (*r_xBeg) = n_x_beg;
if(r_xEnd) (*r_xEnd) = n_x_end;
if(r_yBeg) (*r_yBeg) = n_y_beg;
if(r_yEnd) (*r_yEnd) = n_y_end;
if(n_x_beg == 0 && n_x_end == xLen - 1) return YCX;
if(n_y_beg == 0 && n_y_end == yLen - 1) return XCY;
if(n_y_beg == 0 && n_x_end == xLen - 1) return X2Y;
if(n_x_beg == 0 && n_y_end == yLen - 1) return Y2X;
return XCY;
}
uint64_t get_pair_hap_coverage(uint64_t* readIDs, uint32_t Len, ma_hit_t_alloc* sources, ma_sub_t* coverage_cut)
{
uint32_t m, n, qn;
ma_hit_t *h;
uint64_t R_bases = 0, C_bases = 0;
for (m = 0; m < Len; m++)
{
qn = readIDs[m]>>33;
R_bases += coverage_cut[qn].e - coverage_cut[qn].s;
for (n = 0; n < (uint64_t)(sources[qn].length); n++)
{
h = &(sources[qn].buffer[n]);
C_bases += Get_qe((*h)) - Get_qs((*h));
}
}
return C_bases/R_bases;
}
void get_pair_hap_similarity(uint64_t* readIDs, uint32_t Len, uint32_t target_uId,
ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, double* Match, double* Total)
{
#define CUTOFF_THRES 100
uint32_t i, j, qn, tn, is_Unitig, uId, min_count = 0, max_count = 0, cutoff = 0;;
for (i = 0; i < Len; i++)
{
if(cutoff > CUTOFF_THRES)
{
max_count = 0;
min_count = Len;
break;
}
qn = readIDs[i]>>33;
if(reverse_sources[qn].length > 0) min_count++;
for (j = 0; j < reverse_sources[qn].length; j++)
{
tn = Get_tn(reverse_sources[qn].buffer[j]);
if(read_g->seq[tn].del == 1)
{
get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
}
get_R_to_U(ruIndex, tn, &uId, &is_Unitig);
if(uId!=(uint32_t)-1 && is_Unitig == 1 && uId == target_uId)
{
max_count++;
break;
}
}
//means no match
if(j == reverse_sources[qn].length)
{
cutoff++;
}
else
{
cutoff = 0;
}
}
(*Match) = max_count;
(*Total) = min_count;
}
/**
void get_pair_hap_similarity_deduplicate(uint64_t* readIDs, uint32_t Len, uint32_t target_uId,
ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, double* Match, double* Total)
{
get_pair_hap_similarity(readIDs, Len, target_uId, reverse_sources, read_g, ruIndex, Match, Total);
return;
#define CUTOFF_THRES 100
uint32_t i, j, qn, tn, is_Unitig, uId, min_count = 0, max_count = 0, cutoff = 0, is_found;
for (i = 0; i < Len; i++)
{
if(cutoff > CUTOFF_THRES)
{
max_count = 0;
min_count = Len;
break;
}
qn = readIDs[i]>>33;
is_found = 0;
for (j = 0; j < reverse_sources[qn].length; j++)
{
tn = Get_tn(reverse_sources[qn].buffer[j]);
if(read_g->seq[tn].del == 1)
{
get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
}
get_R_to_U(ruIndex, tn, &uId, &is_Unitig);
if(uId!=(uint32_t)-1 && is_Unitig == 1 && uId == target_uId)
{
max_count++;
}
min_count++;
is_found = 1;
}
//means there is a match
if(is_found)
{
cutoff = 0;
}
else
{
cutoff++;
}
}
(*Match) = max_count;
(*Total) = min_count;
}
**/
inline void check_hap_match(uint32_t qn, uint32_t targetBeg, uint32_t targetEnd, uint32_t targetID,
uint64_t* position_index, ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, uint32_t* is_found, uint32_t* is_match)
{
uint32_t j, tn, uId, is_Unitig, offset;
(*is_found) = (*is_match) = 0;
if(reverse_sources[qn].length > 0) (*is_found) = 1;
for (j = 0; j < reverse_sources[qn].length; j++)
{
tn = Get_tn(reverse_sources[qn].buffer[j]);
if(read_g->seq[tn].del == 1)
{
get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
}
get_R_to_U(ruIndex, tn, &uId, &is_Unitig);
if(uId!=(uint32_t)-1 && is_Unitig == 1 && uId == targetID)
{
offset = (uint32_t)(position_index[tn]);
if(offset >= targetBeg && offset <= targetEnd)
{
(*is_match) = 1;
break;
}
}
}
}
/**
inline void check_hap_match_deduplicate(uint32_t qn, uint32_t targetBeg, uint32_t targetEnd, uint32_t targetID,
uint64_t* position_index, ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, uint32_t* is_found, uint32_t* is_match)
{
check_hap_match(qn, targetBeg, targetEnd, targetID, position_index, reverse_sources, read_g,
ruIndex, is_found, is_match);
return;
uint32_t j, tn, uId, is_Unitig, offset;