From a2884151117fb52cfafc32bcb326aefe6f55d7f6 Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Wed, 8 Apr 2020 16:55:04 -0400 Subject: [PATCH] bug fixing for purge_dup --- Assembly.cpp | 2 +- Overlaps.cpp | 12 +-- Purge_Dups.cpp | 225 ++++++++++++++++++++++++++++++++++++------------- Purge_Dups.h | 2 +- 4 files changed, 175 insertions(+), 66 deletions(-) diff --git a/Assembly.cpp b/Assembly.cpp index 72d211d..3f7b0c8 100644 --- a/Assembly.cpp +++ b/Assembly.cpp @@ -1189,6 +1189,6 @@ int ha_assemble(void) build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf, R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round, asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded); - ///destory_All_reads(&R_INF); + destory_All_reads(&R_INF); return 0; } diff --git a/Overlaps.cpp b/Overlaps.cpp index fa3deb6..e938e40 100644 --- a/Overlaps.cpp +++ b/Overlaps.cpp @@ -22194,6 +22194,8 @@ char* output_file_name, ma_hit_t_alloc** reverse_sources, R_to_U* ruIndex) return 0; } + R_INF.paf = (*sources); R_INF.reverse_paf = (*reverse_sources); + return 1; } @@ -22276,7 +22278,8 @@ kvec_asg_arc_t_warp* new_rtg_edges) - + + enable_debug_mode(1); purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang, min_ovlp, bubble_dist, drop_ratio, 0); @@ -22286,28 +22289,25 @@ kvec_asg_arc_t_warp* new_rtg_edges) - rescue_missing_overlaps_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, min_ovlp, 0, 0, 1, NULL); - renew_utg(ug, read_g, new_rtg_edges); rescue_contained_reads_aggressive(*ug, read_g, sources, coverage_cut, ruIndex, max_hang, min_ovlp, 0, 10, 0, 1, NULL, NULL); - renew_utg(ug, read_g, new_rtg_edges); + ///debug_purge_dup = 1; ///deduplicate_advance(*ug, read_g, coverage_cut, sources, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, 0); ///delete_useless_nodes(ug); - enable_debug_mode(); + enable_debug_mode(0); purge_dups(*ug, read_g, coverage_cut, reverse_sources, ruIndex, new_rtg_edges, 0.75, 50, 50, 0.5, max_hang, min_ovlp, bubble_dist, drop_ratio, 0); delete_useless_nodes(ug); renew_utg(ug, read_g, new_rtg_edges); - ///set_drop_trio_flag(*ug); n_vtx = read_g->n_seq; for (v = 0; v < n_vtx; v++) diff --git a/Purge_Dups.cpp b/Purge_Dups.cpp index 6f5e78b..b976330 100644 --- a/Purge_Dups.cpp +++ b/Purge_Dups.cpp @@ -97,8 +97,6 @@ void init_hap_alignment_struct(hap_alignment_struct* x, uint32_t size) kv_init(x->u_vecs.a); kv_init(x->u_buffer.a); kv_init(x->u_can.a); - - } void destory_hap_alignment_struct(hap_alignment_struct* x) @@ -176,9 +174,9 @@ void init_hap_overlaps_list(hap_overlaps_list* x, uint32_t num) } } -void enable_debug_mode() +void enable_debug_mode(uint32_t mode) { - debug_enable = 1; + debug_enable = mode; } void destory_hap_overlaps_list(hap_overlaps_list* x) @@ -469,6 +467,7 @@ ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, double* Match, { max_count = 0; min_count = Len; + break; } qn = readIDs[i]>>33; if(reverse_sources[qn].length > 0) min_count++; @@ -504,6 +503,60 @@ ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U* ruIndex, double* Match, (*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) @@ -535,6 +588,42 @@ uint64_t* position_index, ma_hit_t_alloc* reverse_sources, asg_t *read_g, R_to_U } +/** +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; + (*is_found) = (*is_match) = 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 == targetID) + { + offset = (uint32_t)(position_index[tn]); + if(offset >= targetBeg && offset <= targetEnd) + { + (*is_match)++; + } + } + (*is_found)++; + } + +} +**/ void determin_hap_alignment_boundary_single_side(uint64_t* readIDs, long long queryLen, long long targetBeg, long long targetEnd, long long targetID, long long eMatch, long long eTotal, long long dir, @@ -554,6 +643,7 @@ R_to_U* ruIndex, uint32_t* n_matchLen, uint32_t* n_max_count, uint32_t* n_min_co { check_hap_match(readIDs[i]>>33, targetBeg, targetEnd, targetID, position_index, reverse_sources, read_g, ruIndex, &is_found, &is_match); + min_count += is_found; max_count += is_match; if(max_count > min_count*Hap_rate) maxId = i; @@ -564,6 +654,8 @@ R_to_U* ruIndex, uint32_t* n_matchLen, uint32_t* n_max_count, uint32_t* n_min_co { check_hap_match(readIDs[i]>>33, targetBeg, targetEnd, targetID, position_index, reverse_sources, read_g, ruIndex, &is_found, &is_match); + + ///if(is_found > 0 && is_match > 0 && is_match > is_found*Hap_rate) if(is_found == 1 && is_match == 1) { break; @@ -580,6 +672,7 @@ R_to_U* ruIndex, uint32_t* n_matchLen, uint32_t* n_max_count, uint32_t* n_min_co { check_hap_match(readIDs[i]>>33, targetBeg, targetEnd, targetID, position_index, reverse_sources, read_g, ruIndex, &is_found, &is_match); + min_count += is_found; max_count += is_match; if(max_count > min_count*Hap_rate) maxId = i; @@ -589,6 +682,8 @@ R_to_U* ruIndex, uint32_t* n_matchLen, uint32_t* n_max_count, uint32_t* n_min_co { check_hap_match(readIDs[i]>>33, targetBeg, targetEnd, targetID, position_index, reverse_sources, read_g, ruIndex, &is_found, &is_match); + + ///if(is_found > 0 && is_match > 0 && is_match > is_found*Hap_rate) if(is_found == 1 && is_match == 1) { break; @@ -823,10 +918,10 @@ uint64_t* position_index, ma_utg_t* xReads, ma_utg_t* yReads) void get_base_boundary(R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, asg_t *read_g, uint64_t* position_index, int max_hang, int min_ovlp, ma_utg_t *xReads, ma_utg_t *yReads, -uint32_t xUid, uint32_t yUid, long long begIndex, long long endIndex, uint32_t dir, uint32_t rev, -uint32_t* x_off, uint32_t* y_off) +uint32_t xUid, uint32_t yUid, long long xBegIndex, long long xEndIndex, long long yBegIndex, long long yEndIndex, +uint32_t dir, uint32_t rev, uint32_t* x_off, uint32_t* y_off) { - long long k, j; + long long k, j, offset; ma_hit_t_alloc *xR = NULL; ma_hit_t *h = NULL; ma_sub_t *sq = NULL, *st = NULL; @@ -837,7 +932,7 @@ uint32_t* x_off, uint32_t* y_off) (*x_off) = (*y_off) = (uint32_t)-1; if(dir == 1) { - for (k = endIndex; k >= begIndex; k--) + for (k = xEndIndex; k >= xBegIndex; k--) { xR = &(reverse_sources[xReads->a[k]>>33]); is_found = 0; oLen = 0; @@ -875,6 +970,11 @@ uint32_t* x_off, uint32_t* y_off) if(rev == 0 && v_dir != w_dir) continue; if(rev == 1 && v_dir == w_dir) continue; + /****************************may have bugs********************************/ + offset = (uint32_t)(position_index[rId]); + if(offset < yBegIndex || offset > yEndIndex) continue; + /****************************may have bugs********************************/ + tmp = get_xy_pos(read_g, &t, v, w, xReads->len, yReads->len, position_index, &(t.el)); if(((tmp>>32) == (uint32_t)-1) || (((uint32_t)tmp) == (uint32_t)-1)) continue; @@ -893,7 +993,7 @@ uint32_t* x_off, uint32_t* y_off) } else { - for (k = begIndex; k <= endIndex; k++) + for (k = xBegIndex; k <= xEndIndex; k++) { xR = &(reverse_sources[xReads->a[k]>>33]); is_found = 0; oLen = 0; @@ -930,8 +1030,11 @@ uint32_t* x_off, uint32_t* y_off) w_dir = (t.v == w)?1:0; if(rev == 0 && v_dir != w_dir) continue; if(rev == 1 && v_dir == w_dir) continue; - - + + /****************************may have bugs********************************/ + offset = (uint32_t)(position_index[rId]); + if(offset < yBegIndex || offset > yEndIndex) continue; + /****************************may have bugs********************************/ tmp = get_xy_pos(read_g, &t, v, w, xReads->len, yReads->len, position_index, &(t.el)); if(((tmp>>32) == (uint32_t)-1) || (((uint32_t)tmp) == (uint32_t)-1)) continue; @@ -963,11 +1066,12 @@ long long* r_x_pos_beg, long long* r_x_pos_end, long long* r_y_pos_beg, long lon uint32_t x_pos_beg, y_pos_beg, x_pos_end, y_pos_end; /*************************x***************************/ get_base_boundary(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), 0, - Get_rev(*hap_can), &x_pos_beg, &y_pos_beg); + 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), 0, Get_rev(*hap_can), &x_pos_beg, &y_pos_beg); + get_base_boundary(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), 1, - Get_rev(*hap_can), &x_pos_end, &y_pos_end); + 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), 1, Get_rev(*hap_can), &x_pos_end, &y_pos_end); /*************************x***************************/ if(x_pos_beg == (uint32_t)-1 || y_pos_beg == (uint32_t)-1 @@ -1033,6 +1137,7 @@ long long* r_y_pos_beg, long long* r_y_pos_end) ///flag = classify_hap_overlap(xBasePos, xBasePos, xReads->len, yBasePos, yBasePos, yReads->len); flag = vote_overlap_type(u_buffer, hap_can, position_index, xReads, yReads); + if(flag == XCY) { get_pair_hap_similarity(yReads->a, yLen, xUid, reverse_sources, read_g, ruIndex, @@ -1065,7 +1170,6 @@ long long* r_y_pos_beg, long long* r_y_pos_end) max_count = xLeftMatch + yRightMatch; min_count = xLeftTotal + yRightTotal; } else abort(); - hap_can->weight = hap_can->index_beg = 0; if(min_count == 0) return NON_PLOID; @@ -1100,6 +1204,8 @@ long long* r_y_pos_beg, long long* r_y_pos_end) hap_can->index_end = determine_hap_overlap_type(hap_can, xReads, yReads, ruIndex, reverse_sources, coverage_cut, read_g, position_index, max_hang, min_ovlp, xUid, yUid, r_x_pos_beg, r_x_pos_end, r_y_pos_beg, r_y_pos_end); + 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; if(hap_can->index_end == (uint32_t)-1) return NON_PLOID; return PLOID; @@ -1111,9 +1217,11 @@ long long* r_y_pos_beg, long long* r_y_pos_end) void print_hap_paf(ma_ug_t *ug, hap_overlaps* ovlp) { - fprintf(stderr, "utg%.6d%c\t%u\t%u\t%u\t%c\tutg%.6d%c\t%u\t%u\t%u\t%u\t%u\n", - ovlp->xUid+1, "lc"[ug->u.a[ovlp->xUid].circ], ug->u.a[ovlp->xUid].len, ovlp->x_beg_pos, ovlp->x_end_pos, "+-"[ovlp->rev], - ovlp->yUid+1, "lc"[ug->u.a[ovlp->yUid].circ], ug->u.a[ovlp->yUid].len, ovlp->y_beg_pos, ovlp->y_end_pos, ovlp->type, (uint32_t)ovlp->weight); + fprintf(stderr, "utg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%c\tutg%.6d%c\t%u(%u)\t%u(%u)\t%u(%u)\t%u\t%u\n", + ovlp->xUid+1, "lc"[ug->u.a[ovlp->xUid].circ], ug->u.a[ovlp->xUid].len, ug->u.a[ovlp->xUid].n, + ovlp->x_beg_pos, ovlp->x_beg_id, ovlp->x_end_pos, ovlp->x_end_id, "+-"[ovlp->rev], + ovlp->yUid+1, "lc"[ug->u.a[ovlp->yUid].circ], ug->u.a[ovlp->yUid].len, ug->u.a[ovlp->yUid].n, + ovlp->y_beg_pos, ovlp->y_beg_id, ovlp->y_end_pos, ovlp->y_end_id, ovlp->type, (uint32_t)ovlp->weight); } void hap_alignment(ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* reverse_sources, @@ -1197,18 +1305,6 @@ hap_overlaps_list* all_ovlp) xReads = &(ug->u.a[xUid]); yReads = &(ug->u.a[yUid]); u_buffer->a.n = 0; - - - //if(xUid == 404 && yUid == 307) - // if(xReads->n <= 100 && yReads->n <= 100) - // { - // debug_enable = 1; - // } - // else - // { - // debug_enable = 0; - // } - // debug_enable = 1; for (k = 0; k < xReads->n; k++) { @@ -1263,12 +1359,6 @@ hap_overlaps_list* all_ovlp) } if(u_buffer->a.n == 0) continue; - - // if(debug_enable) - // { - // print_debug_unitig(xReads, position_index, "xReads"); - // print_debug_unitig(yReads, position_index, "yReads"); - // } qsort(u_buffer->a.a, u_buffer->a.n, sizeof(asg_arc_t_offset), cmp_hap_alignment); k = 0; @@ -1500,18 +1590,6 @@ static void hap_alignment_worker(void *_data, long eid, int tid) xReads = &(ug->u.a[xUid]); yReads = &(ug->u.a[yUid]); u_buffer->a.n = 0; - - - //if(xUid == 404 && yUid == 307) - // if(xReads->n <= 100 && yReads->n <= 100) - // { - // debug_enable = 1; - // } - // else - // { - // debug_enable = 0; - // } - // debug_enable = 1; for (k = 0; k < xReads->n; k++) { @@ -1947,10 +2025,10 @@ void clean_purge_graph(asg_t *purge_g, int max_dist, float drop_ratio) void get_node_boundary(R_to_U* ruIndex, ma_hit_t_alloc* reverse_sources, ma_sub_t *coverage_cut, asg_t *read_g, uint64_t* position_index, int max_hang, int min_ovlp, ma_utg_t *xReads, ma_utg_t *yReads, -uint32_t xUid, uint32_t yUid, long long begIndex, long long endIndex, uint32_t dir, uint32_t rev, -asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) +uint32_t xUid, uint32_t yUid, long long xBegIndex, long long xEndIndex, long long yBegIndex, +long long yEndIndex, uint32_t dir, uint32_t rev, asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) { - long long k, j; + long long k, j, offset; ma_hit_t_alloc *xR = NULL; ma_hit_t *h = NULL; ma_sub_t *sq = NULL, *st = NULL; @@ -1960,7 +2038,7 @@ asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) reture_t_f->del = reture_t_r->del = 1; if(dir == 1) { - for (k = endIndex; k >= begIndex; k--) + for (k = xEndIndex; k >= xBegIndex; k--) { xR = &(reverse_sources[xReads->a[k]>>33]); is_found = 0; @@ -1997,6 +2075,12 @@ asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) if(rev == 0 && v_dir != w_dir) continue; if(rev == 1 && v_dir == w_dir) continue; if(v_dir == 1) continue; + + /****************************may have bugs********************************/ + offset = (uint32_t)(position_index[rId]); + if(offset < yBegIndex || offset > yEndIndex) continue; + /****************************may have bugs********************************/ + /************************get reverse edge*************************/ index = get_specific_overlap(&(reverse_sources[Get_tn(*h)]), Get_tn(*h), Get_qn(*h)); if(index == -1) continue; @@ -2023,7 +2107,7 @@ asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) } else { - for (k = begIndex; k <= endIndex; k++) + for (k = xBegIndex; k <= xEndIndex; k++) { xR = &(reverse_sources[xReads->a[k]>>33]); is_found = 0; oLen = 0; @@ -2061,6 +2145,11 @@ asg_arc_t* reture_t_f, asg_arc_t* reture_t_r) if(rev == 0 && v_dir != w_dir) continue; if(rev == 1 && v_dir == w_dir) continue; if(v_dir == 0) continue; + + /****************************may have bugs********************************/ + offset = (uint32_t)(position_index[rId]); + if(offset < yBegIndex || offset > yEndIndex) continue; + /****************************may have bugs********************************/ /************************get reverse edge*************************/ index = get_specific_overlap(&(reverse_sources[Get_tn(*h)]), Get_tn(*h), Get_qn(*h)); @@ -2260,7 +2349,8 @@ uint64_t* position_index, int max_hang, int min_ovlp, kvec_asg_arc_t_warp* edge, if(cut_end < endIndex) endIndex = cut_end; get_node_boundary(ruIndex, reverse_sources, coverage_cut, read_g, position_index, max_hang, - min_ovlp, xReads, yReads, v>>1, w>>1, begIndex, endIndex, v&1, x->rev, &t_forward, &t_backward); + min_ovlp, xReads, yReads, v>>1, w>>1, begIndex, endIndex, x->y_beg_id, x->y_end_id-1, v&1, + x->rev, &t_forward, &t_backward); if(t_forward.del || t_backward.del) break; kv_push(asg_arc_t, edge->a, t_forward); @@ -2387,12 +2477,26 @@ uint64_t* position_index, int max_hang, int min_ovlp, kvec_asg_arc_t_warp* edge, } free(b_0.b.a); } + +void print_all_purge_ovlp(ma_ug_t *ug, hap_overlaps_list* all_ovlp) +{ + uint32_t v, uId, i; + for (v = 0; v < all_ovlp->num; v++) + { + uId = v; + if(uId != 96 && uId != 272) continue; + for (i = 0; i < all_ovlp->x[uId].a.n; i++) + { + print_hap_paf(ug, &(all_ovlp->x[uId].a.a[i])); + } + } + +} void purge_dups(ma_ug_t *ug, asg_t *read_g, ma_sub_t* coverage_cut, ma_hit_t_alloc* reverse_sources, R_to_U* ruIndex, kvec_asg_arc_t_warp* edge, float density, uint32_t bi_graph_Len, uint32_t long_hap_overlap, float lable_match_rate, int max_hang, int min_ovlp, long long bubble_dist, float drop_ratio, uint32_t just_contain) { - fprintf(stderr, "*****************\n"); asg_t *purge_g = NULL; purge_g = asg_init(); asg_t* nsg = ug->g; @@ -2472,6 +2576,9 @@ uint32_t just_contain) kt_for(asm_opt.thread_num, hap_alignment_worker, &hap_buf, nsg->n_seq); + ///if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp); + + // for (v = 0; v < nsg->n_seq; v++) // { // uId = v; @@ -2550,7 +2657,10 @@ uint32_t just_contain) asg_symm(purge_g); clean_purge_graph(purge_g, bubble_dist, drop_ratio); - ///if(debug_enable) print_purge_gfa(ug, purge_g); + + // if(debug_enable) print_purge_gfa(ug, purge_g); + // if(debug_enable) print_all_purge_ovlp(ug, &all_ovlp); + link_unitigs(purge_g, ug, &all_ovlp, ruIndex, reverse_sources, coverage_cut, read_g, position_index, max_hang, min_ovlp, edge, hap_buf.buf[0].visit); } @@ -2582,6 +2692,5 @@ uint32_t just_contain) // free(vote_counting); // free(visit); destory_hap_alignment_struct_pip(&hap_buf); - fprintf(stderr, "#################\n"); } diff --git a/Purge_Dups.h b/Purge_Dups.h index e9e3152..07fa0d8 100644 --- a/Purge_Dups.h +++ b/Purge_Dups.h @@ -14,6 +14,6 @@ uint32_t just_contain); void fill_unitig(uint64_t* buffer, uint32_t bufferLen, asg_t* read_g, kvec_asg_arc_t_warp* edge, uint32_t is_circle, uint64_t* rLen); -void enable_debug_mode(); +void enable_debug_mode(uint32_t mode); #endif \ No newline at end of file