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update r311

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chhylp123
2021-02-14 13:32:02 -05:00
parent c47a1df4b0
commit d2bf15eba4
3 changed files with 6 additions and 52 deletions
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CommandLines.h
+1 -1
View File
@@ -3,7 +3,7 @@
#include <pthread.h>
#define HA_VERSION "0.14-r310"
#define HA_VERSION "0.14-r311"
#define VERBOSE 0
Overlaps.cpp
+1 -8
View File
@@ -11553,10 +11553,9 @@ kvec_asg_arc_t_warp* new_rtg_edges, int max_hang, int min_ovlp)
uint8_t* primary_flag = (uint8_t*)calloc(sg->n_seq, sizeof(uint8_t));
int tmp_cov = asm_opt.hom_global_coverage;
asm_opt.hom_global_coverage = -1;
fprintf(stderr, "xxx-0-xxx\n");
purge_dups(ug, sg, coverage_cut, sources, reverse_sources, ruIndex, new_rtg_edges,
asm_opt.purge_simi_rate, asm_opt.purge_overlap_len, max_hang, min_ovlp, 0, 0, 0, 1, NULL);
fprintf(stderr, "xxx-1-xxx\n");
dip_thre_max = ((double)asm_opt.hom_global_coverage)/((double)HOM_PEAK_RATE)*0.70;
asm_opt.hom_global_coverage = tmp_cov;
///fprintf(stderr, "dip_thre_max: %lu\n", dip_thre_max);
@@ -25201,10 +25200,8 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, uint32_t chai
memset(&bub, 0, sizeof(bubble_type));
copy_ug = copy_untig_graph(ug);
fprintf(stderr, "\nstart: sbsbsb-0-sbsbsb\n");
reset_bub(&bub, ug, sg, copy_ug, &link, &copy_link, ruIndex, coverage_cut, sources,
reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
fprintf(stderr, "start: sbsbsb-0-sbsbsb\n");
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_contained_reads(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_1.hic", sources, ruIndex, max_hang, min_ovlp);
@@ -25212,20 +25209,16 @@ float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, uint32_t chai
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
fprintf(stderr, "\nstart: sbsbsb-1-sbsbsb\n");
reset_bub(&bub, ug, sg, copy_ug, &link, &copy_link, ruIndex, coverage_cut, sources,
reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
fprintf(stderr, "start: sbsbsb-1-sbsbsb\n");
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_missing_ovlp(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_2.hic", sources, ruIndex, max_hang, min_ovlp);
ma_ug_destroy(ug); ug = NULL; ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
fprintf(stderr, "\nstart: sbsbsb-2-sbsbsb\n");
reset_bub(&bub, ug, sg, copy_ug, &link, &copy_link, ruIndex, coverage_cut, sources,
reverse_sources, max_hang, min_ovlp, &new_rtg_edges);
fprintf(stderr, "start: sbsbsb-2-sbsbsb\n");
beg_idx = bub.f_bub; occ = bub.b_bub + bub.b_end_bub + bub.tangle_bub;
rescue_bubbles_by_missing_ovlp_backward(ug, sg, sources, coverage_cut, ruIndex, max_hang, min_ovlp, chainLenThres, beg_idx, occ, &bub);
///output_unitig_graph(sg, coverage_cut, (char*)"debug_3.hic", sources, ruIndex, max_hang, min_ovlp);
Purge_Dups.cpp
+4 -43
View File
@@ -1500,18 +1500,6 @@ void quick_LIS(asg_arc_t_offset* x, uint32_t n, kvec_t_i32_warp* tailIndex, kvec
tailIndex->a.a[0] = 0;
prevIndex->a.a[0] = -1;
/*******************************for debug************************************/
if(n == 3)
{
fprintf(stderr, "n=%u\n", n);
for(i = 0; i < (long long)n; i++)
{
fprintf(stderr, "i: %lld, Get_xOff: %lld, Get_yOff: %lld\n",
i, Get_xOff(x[i].Off), Get_yOff(x[i].Off));
}
}
/*******************************for debug************************************/
///x has already sorted by x_pos
for(i = 1; i < (long long)n; i++)
{
@@ -1532,13 +1520,6 @@ void quick_LIS(asg_arc_t_offset* x, uint32_t n, kvec_t_i32_warp* tailIndex, kvec
// future subsequence
// It will replace ceil value in tailIndices
pos = GetCeilIndex(x, tailIndex, -1, len - 1, Get_yOff(x[i].Off));
/*******************************for debug************************************/
if(n == 3)
{
fprintf(stderr, "++++i: %lld, Get_xOff: %lld, Get_yOff: %lld, pos: %lld\n",
i, Get_xOff(x[i].Off), Get_yOff(x[i].Off), pos);
}
/*******************************for debug************************************/
prevIndex->a.a[i] = pos > 0? tailIndex->a.a[pos - 1] : -1;
tailIndex->a.a[pos] = i;
}
@@ -1644,9 +1625,7 @@ uint32_t* xBeg, uint32_t* xEnd, uint32_t* yBeg, uint32_t* yEnd)
u_buffer->a.n = m;
///print_asg_arc_t_offset(u_buffer->a.a, u_buffer->a.n, "after");
fprintf(stderr, "+sbsbsbsbsbsb-quick_LIS, u_buffer->a.n: %u\n", (uint32_t)u_buffer->a.n);
quick_LIS(u_buffer->a.a, u_buffer->a.n, tailIndex, prevIndex);
fprintf(stderr, "-sbsbsbsbsbsb-quick_LIS, u_buffer->a.n: %u\n", (uint32_t)u_buffer->a.n);
if(tailIndex->a.n == 0) return;
@@ -1664,13 +1643,10 @@ kvec_t_i32_warp* prevIndex, long long* r_x_pos_beg, long long* r_x_pos_end, long
{
uint32_t x_pos_beg, y_pos_beg, x_pos_end, y_pos_end;
/*************************x***************************/
fprintf(stderr, "+sbsbsbsbsbsb-xUid: %u, yUid: %u, Get_x_beg(*hap_can): %u, Get_x_end(*hap_can): %u, Get_y_beg(*hap_can): %u, Get_y_end(*hap_can): %u, Get_rev(*hap_can): %u\n",
xUid, yUid, Get_x_beg(*hap_can), Get_x_end(*hap_can), Get_y_beg(*hap_can), Get_y_end(*hap_can), Get_rev(*hap_can));
get_base_boundary_advance(ruIndex, reverse_sources, coverage_cut, read_g, position_index,
max_hang, min_ovlp, xReads, yReads, xUid, yUid, Get_x_beg(*hap_can), Get_x_end(*hap_can),
Get_y_beg(*hap_can), Get_y_end(*hap_can), Get_rev(*hap_can), u_buffer, tailIndex, prevIndex,
&x_pos_beg, &x_pos_end, &y_pos_beg, &y_pos_end);
fprintf(stderr, "-sbsbsbsbsbsb-xUid: %u, yUid: %u\n", xUid, yUid);
/*************************x***************************/
if(x_pos_beg == (uint32_t)-1 || y_pos_beg == (uint32_t)-1
@@ -1948,12 +1924,10 @@ long long* r_x_pos_beg, long long* r_x_pos_end, long long* r_y_pos_beg, long lon
hap_can->y_beg_pos = r_y_interval_beg;
hap_can->y_end_pos = r_y_interval_end;
fprintf(stderr, "+inner-xUid: %u, yUid: %u\n", xUid, yUid);
hap_can->index_end = determine_hap_overlap_type_advance(hap_can, xReads, yReads,
ruIndex, reverse_sources, coverage_cut, read_g, position_index, max_hang, min_ovlp,
xUid, yUid, u_buffer, tailIndex, prevIndex, r_x_pos_beg, r_x_pos_end, r_y_pos_beg,
r_y_pos_end);
fprintf(stderr, "-inner-xUid: %u, yUid: %u\n", xUid, yUid);
if(hap_can->index_end == XCY && yReads->len > (xReads->len*2)) return NON_PLOID;
if(hap_can->index_end == YCX && xReads->len > (yReads->len*2)) return NON_PLOID;
@@ -2825,7 +2799,6 @@ void hap_alignment_worker(void *_data, long eid, int tid)
static void hap_alignment_advance_worker(void *_data, long eid, int tid)
{
fprintf(stderr, "\neid: %ld, tid: %d\n", eid, tid);
hap_alignment_struct_pip* hap_buf = (hap_alignment_struct_pip*)_data;
ma_ug_t *ug = hap_buf->ug;
asg_t *read_g = hap_buf->read_g;
@@ -2997,20 +2970,14 @@ static void hap_alignment_advance_worker(void *_data, long eid, int tid)
is_update = 0;
if(u_can->a.a[k].weight < Get_match(hap_can)*Hap_rate) continue;
fprintf(stderr, "+k: %u, u_can->a.n: %u, xUid: %u, yUid: %u\n",
k, (uint32_t)u_can->a.n, xUid, yUid);
if(calculate_pair_hap_similarity_advance(&(u_can->a.a[k]), position_index, xUid, yUid,
xReads, yReads, sources, reverse_sources, read_g, ruIndex, coverage_cut, Hap_rate, max_hang,
min_ovlp, cov_threshold, u_buffer, score_vc, prevIndex_vec, &r_x_pos_beg, &r_x_pos_end,
&r_y_pos_beg, &r_y_pos_end)!=PLOID)
{
fprintf(stderr, "-0-k: %u, u_can->a.n: %u, xUid: %u, yUid: %u\n",
k, (uint32_t)u_can->a.n, xUid, yUid);
continue;
}
fprintf(stderr, "-1-k: %u, u_can->a.n: %u, xUid: %u, yUid: %u\n",
k, (uint32_t)u_can->a.n, xUid, yUid);
if(Get_match(hap_can) < Get_match(u_can->a.a[k]))
{
@@ -4212,13 +4179,8 @@ uint32_t minLen, double purge_threshold)
{
asg_t* nsg = ug->g;
uint64_t v, k, total_bases = 0, alter_bases = 0, primary_bases = 0, purge_bases = 0;
/*******************************for debug************************************/
fprintf(stderr, "bbb-0-bbb\n");
fprintf(stderr, "asm_opt.thread_num: %d\n", asm_opt.thread_num);
///kt_for(asm_opt.thread_num, hap_alignment_advance_worker, hap_buf, nsg->n_seq);
kt_for(1, hap_alignment_advance_worker, hap_buf, nsg->n_seq);
fprintf(stderr, "bbb-1-bbb\n");
/*******************************for debug************************************/
kt_for(asm_opt.thread_num, hap_alignment_advance_worker, hap_buf, nsg->n_seq);
filter_hap_overlaps_by_length(all_ovlp, minLen);
normalize_hap_overlaps_advance(all_ovlp, back_all_ovlp, ug, read_g, reverse_sources, ruIndex);
@@ -4333,7 +4295,7 @@ uint32_t just_contain, uint32_t just_coverage, hc_links* link)
init_hap_alignment_struct_pip(&hap_buf, asm_opt.thread_num, nsg->n_seq, ug, read_g,
sources, reverse_sources, ruIndex, coverage_cut, position_index, density, max_hang, min_ovlp,
0.05, &all_ovlp);
fprintf(stderr, "aaa-0-aaa\n");
if(hap_buf.cov_threshold < 0)
{
if(if_ploid_sample(ug, read_g, ruIndex, sources, reverse_sources, coverage_cut,
@@ -4351,10 +4313,9 @@ uint32_t just_contain, uint32_t just_coverage, hc_links* link)
if(asm_opt.hom_global_coverage == -1) asm_opt.hom_global_coverage = hap_buf.cov_threshold;
fprintf(stderr, "[M::%s] purge duplication coverage threshold: %lld\n", __func__, hap_buf.cov_threshold);
if(just_coverage) goto end_coverage;
fprintf(stderr, "aaa-1-aaa\n");
///kt_for(asm_opt.thread_num, hap_alignment_worker, &hap_buf, nsg->n_seq);
kt_for(asm_opt.thread_num, hap_alignment_advance_worker, &hap_buf, nsg->n_seq);
fprintf(stderr, "aaa-2-aaa\n");
///if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp);