mirror of
https://github.com/chhylp123/hifiasm.git
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for high-het and coverage
This commit is contained in:
chhylp123
+824
-29
@@ -6,7 +6,7 @@
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#include "Levenshtein_distance.h"
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#include "Assembly.h"
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#include "CommandLines.h"
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///#include "ksw2.h"
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#include "ksw2.h"
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@@ -7483,39 +7483,46 @@ void add_existing_cell_to_cigar_record_with_different_base(Cigar_record* dummy,
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}
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}
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void afine_gap_alignment(const char *tseq, uint8_t* tnum, const int tl,
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const char *qseq, uint8_t* qnum, const int ql, const uint8_t *c2n, const int strand,
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void afine_gap_alignment(const char *qseq, uint8_t* qnum, const int ql,
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const char *tseq, uint8_t* tnum, const int tl, const uint8_t *c2n, const int strand,
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int sc_mch, int sc_mis, int gapo, int gape, int bandLen, int zdrop, int end_bonus,
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long long* max_t_pos, long long* max_q_pos, long long* score, long long* droped)
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long long* max_q_pos, long long* max_t_pos, long long* global_score,
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long long* extention_score, long long* q_boundary_score, long long* q_boundary_t_coordinate,
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long long* t_boundary_score, long long* t_boundary_q_coordinate,
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long long* droped, int mode)
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{
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/**************for ksw2**************/
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// (*max_t_pos) = (*max_q_pos) = -1;
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// int i, a = sc_mch, b = sc_mis < 0? sc_mis : -sc_mis; // a>0 and b<0
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(*max_t_pos) = (*max_q_pos) = -1;
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int i, a = sc_mch, b = sc_mis < 0? sc_mis : -sc_mis; // a>0 and b<0
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// int8_t mat[25] = {(int8_t)a,(int8_t)b,(int8_t)b,(int8_t)b,0,
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// (int8_t)b,(int8_t)a,(int8_t)b,(int8_t)b,0, (int8_t)b,(int8_t)b,(int8_t)a,(int8_t)b,0,
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// (int8_t)b,(int8_t)b,(int8_t)b,(int8_t)a,0, 0,0,0,0,0};
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// ksw_extz_t ez;
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// memset(&ez, 0, sizeof(ksw_extz_t));
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int8_t mat[25] = {(int8_t)a,(int8_t)b,(int8_t)b,(int8_t)b,0,
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(int8_t)b,(int8_t)a,(int8_t)b,(int8_t)b,0, (int8_t)b,(int8_t)b,(int8_t)a,(int8_t)b,0,
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(int8_t)b,(int8_t)b,(int8_t)b,(int8_t)a,0, 0,0,0,0,0};
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ksw_extz_t ez;
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memset(&ez, 0, sizeof(ksw_extz_t));
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// if(strand == FORWARD_KSW)
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// {
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// for (i = 0; i < tl; ++i) tnum[i] = c2n[(uint8_t)tseq[i]]; // encode to 0/1/2/3
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// for (i = 0; i < ql; ++i) qnum[i] = c2n[(uint8_t)qseq[i]];
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// }
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// else if(strand == BACKWARD_KSW)
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// {
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// for (i = 0; i < tl; ++i) tnum[i] = c2n[(uint8_t)tseq[tl - i - 1]]; // encode to 0/1/2/3
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// for (i = 0; i < ql; ++i) qnum[i] = c2n[(uint8_t)qseq[ql - i - 1]];
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// }
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// ksw_extz2_sse(0, ql, qnum, tl, tnum, 5, mat, gapo, gape, bandLen, zdrop, end_bonus, 0, &ez);
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// (*score) = ez.max;
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// (*max_t_pos) = ez.max_t;
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// (*max_q_pos) = ez.max_q;
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// (*droped) = ez.zdropped;
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// free(ez.cigar);
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if(strand == FORWARD_KSW)
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{
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for (i = 0; i < tl; ++i) tnum[i] = c2n[(uint8_t)tseq[i]]; // encode to 0/1/2/3
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for (i = 0; i < ql; ++i) qnum[i] = c2n[(uint8_t)qseq[i]];
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}
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else if(strand == BACKWARD_KSW)
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{
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for (i = 0; i < tl; ++i) tnum[i] = c2n[(uint8_t)tseq[tl - i - 1]]; // encode to 0/1/2/3
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for (i = 0; i < ql; ++i) qnum[i] = c2n[(uint8_t)qseq[ql - i - 1]];
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}
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ksw_extz2_sse(0, ql, qnum, tl, tnum, 5, mat, gapo, gape, bandLen, zdrop, end_bonus,
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mode, &ez);
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(*global_score) = ez.score;
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(*extention_score) = ez.max;
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(*q_boundary_score) = ez.mqe;
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(*q_boundary_t_coordinate) = ez.mqe_t;
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(*t_boundary_score) = ez.mte;
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(*t_boundary_q_coordinate) = ez.mte_q;
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(*max_t_pos) = ez.max_t;
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(*max_q_pos) = ez.max_q;
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(*droped) = ez.zdropped;
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free(ez.cigar);
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/**
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for (i = 0; i < ez.n_cigar; ++i) // print CIGAR
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@@ -7524,3 +7531,791 @@ long long* max_t_pos, long long* max_q_pos, long long* score, long long* droped)
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**/
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/**************for ksw2**************/
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}
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int fill_chain_by_affine_gap_debug(Fake_Cigar* chain, char* x_string, char* y_string, overlap_region* ovc,
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long long x_readLen, long long y_readLen, Cigar_record* cigar, uint8_t* c2n, uint8_t* x_num, uint8_t* y_num,
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long long* minus_score_thres, long long* final_scores)
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{
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long long i, xOffset, yOffset, xRegionLen, yRegionLen, /**bandLen,**/ maxXpos, maxYpos, zdroped;
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long long mapGlobalScore, mapExtentScore;
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long long xBuoundaryScore, xBuoundaryYcoordinate, yBuoundaryScore, yBuoundaryXcoordinate;
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///float band_rate = 0.08;
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int endbouns, mode;
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long long xBeg, yBeg;
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xBeg = ovc->x_pos_s;
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yBeg = ovc->y_pos_s;
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if(chain->length <= 0) return 0;
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// long long minus_score_thres = (EstimateOlen*HIGH_HET_ERROR_RATE*(MATCH_SCORE_KSW+(MAX(MISMATCH_SCORE_KSW,GAP_EXT_KSW))));
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// long long total_score_thres = EstimateOlen*MATCH_SCORE_KSW - minus_score_thres;
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long long sum_score = 0, current_ovlp = 0, zdrop_occ = 0;
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long long new_xBeg, new_yBeg, new_xEnd, new_yEnd;
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new_xBeg = ovc->x_pos_s;
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new_yBeg = ovc->y_pos_s;
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new_xEnd = ovc->x_pos_e;
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new_yEnd = ovc->y_pos_e;
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///long long sub_score_sum;
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///deal with region 0 backward
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i = 0;
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endbouns = 0;
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xOffset = get_fake_gap_pos(chain, 0);
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xOffset = xOffset - 1;
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yOffset = (xOffset - xBeg) + yBeg + get_fake_gap_shift(chain, 0);
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if(xOffset >= 0 && yOffset >= 0)
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{
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xRegionLen = xOffset + 1;
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yRegionLen = yOffset + 1;
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//note here cannot use DIFF(xRegionLen, yRegionLen)
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// bandLen = (MIN(xRegionLen, yRegionLen))*band_rate;
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// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
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///do alignment backward
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///for beginning part and end part, must use exact mode
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mode = KSW_EZ_SCORE_ONLY;
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afine_gap_alignment(x_string, x_num, xRegionLen, y_string, y_num, yRegionLen,
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c2n, BACKWARD_KSW, MATCH_SCORE_KSW, MISMATCH_SCORE_KSW, GAP_OPEN_KSW, GAP_EXT_KSW,
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/**bandLen,**/BAND_KSW, Z_DROP_KSW, endbouns, &maxXpos, &maxYpos, &mapGlobalScore,
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&mapExtentScore, &xBuoundaryScore, &xBuoundaryYcoordinate,
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&yBuoundaryScore, &yBuoundaryXcoordinate, &zdroped, mode);
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if(!zdroped)
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{
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if(xRegionLen <= yRegionLen)
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{
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sum_score += xBuoundaryScore;
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new_yBeg = yRegionLen - xBuoundaryYcoordinate - 1;
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}
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else
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{
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sum_score += yBuoundaryScore;
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new_xBeg = xRegionLen - yBuoundaryXcoordinate - 1;
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}
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}
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else
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{ ///return 0;
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sum_score += mapExtentScore;
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if(xRegionLen <= yRegionLen)
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{
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sum_score -= (GAP_OPEN_KSW + (xRegionLen - maxXpos)*GAP_EXT_KSW);
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}
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else
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{
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sum_score -= (GAP_OPEN_KSW + (yRegionLen - maxYpos)*GAP_EXT_KSW);
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}
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}
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}
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///align forward
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for (i = 0; i < (long long)chain->length; i++)
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{
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// xOffset = get_fake_gap_pos(chain, i);
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// yOffset = xOffset + get_fake_gap_shift(chain, i);
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xOffset = get_fake_gap_pos(chain, i);
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yOffset = (xOffset - xBeg) + yBeg + get_fake_gap_shift(chain, i);
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///last region
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if(i == (long long)(chain->length - 1))
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{
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endbouns = 0;
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xRegionLen = x_readLen - xOffset;
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yRegionLen = y_readLen - yOffset;
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///for beginning part and end part, must use exact mode
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mode = KSW_EZ_SCORE_ONLY;
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//note here cannot use DIFF(xRegionLen, yRegionLen)
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// bandLen = (MIN(xRegionLen, yRegionLen))*band_rate;
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// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
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}
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else
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{
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///higher endbouns for middle regions
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endbouns = MATCH_SCORE_KSW;
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xRegionLen = get_fake_gap_pos(chain, i+1) - xOffset;
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yRegionLen = (get_fake_gap_pos(chain, i+1) + get_fake_gap_shift(chain, i+1)) -
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(get_fake_gap_pos(chain, i) + get_fake_gap_shift(chain, i));
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mode = KSW_EZ_SCORE_ONLY | KSW_EZ_APPROX_MAX | KSW_EZ_APPROX_DROP;
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// bandLen = MAX((MIN(xRegionLen, yRegionLen))*band_rate, DIFF(xRegionLen, yRegionLen));
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// if(bandLen == 0) bandLen = MIN(xRegionLen, yRegionLen);
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}
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if(minus_score_thres)
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{
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current_ovlp = MIN((xOffset + 1 - xBeg), (yOffset + 1 - yBeg));
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current_ovlp = current_ovlp*MATCH_SCORE_KSW;
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if(current_ovlp - sum_score > (*minus_score_thres))
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{
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return 0;
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}
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}
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if(xOffset < 0) xOffset = 0;
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if(yOffset < 0) yOffset = 0;
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if(xRegionLen < 0) xRegionLen = 0;
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if(yRegionLen < 0) yRegionLen = 0;
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///do alignment forward
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///text is x, query is y
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afine_gap_alignment(x_string+xOffset, x_num, xRegionLen, y_string+yOffset, y_num, yRegionLen,
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c2n, FORWARD_KSW, MATCH_SCORE_KSW, MISMATCH_SCORE_KSW, GAP_OPEN_KSW, GAP_EXT_KSW,
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/**bandLen,**/BAND_KSW, Z_DROP_KSW, endbouns, &maxXpos, &maxYpos, &mapGlobalScore,
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&mapExtentScore, &xBuoundaryScore, &xBuoundaryYcoordinate,
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&yBuoundaryScore, &yBuoundaryXcoordinate, &zdroped, mode);
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// fprintf(stderr, "# xOffset: %lld, yOffset: %lld, xRegionLen: %lld, yRegionLen: %lld, bandLen: %lld, maxXpos: %lld, maxYpos: %lld, zdroped: %lld\n",
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// xOffset, yOffset, xRegionLen, yRegionLen, BAND_KSW, maxXpos, maxYpos, zdroped);
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if(!zdroped)
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{
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if(i != (long long)(chain->length - 1))
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{
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sum_score += mapGlobalScore;
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}
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else
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{
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if(xRegionLen <= yRegionLen)
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{
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sum_score += xBuoundaryScore;
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new_yEnd = yOffset + xBuoundaryYcoordinate;
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}
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else
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{
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sum_score += yBuoundaryScore;
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new_xEnd = xOffset + yBuoundaryXcoordinate;
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// if(new_xEnd != (long long)ovc->x_pos_e)
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// {
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// fprintf(stderr, "\n******direction: %u, new_xBeg: %lld, new_xEnd: %lld, new_yBeg: %lld, new_yEnd: %lld, old_xBeg: %u, old_xEnd: %u, old_yBeg: %u, old_yEnd: %u\n",
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// ovc->y_pos_strand, new_xBeg, new_xEnd, new_yBeg, new_yEnd, ovc->x_pos_s, ovc->x_pos_e, ovc->y_pos_s, ovc->y_pos_e);
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// fprintf(stderr, "x_readLen: %lld, y_readLen: %lld\n", x_readLen, y_readLen);
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// fprintf(stderr, "xID: %lld, yID: %lld\n", ovc->x_id, ovc->y_id);
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// fprintf(stderr, "xRegionLen: %lld, yRegionLen: %lld\n", xRegionLen, yRegionLen);
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// fprintf(stderr, "xOffset: %lld, yOffset: %lld\n", xOffset, yOffset);
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// fprintf(stderr, "yBuoundaryXcoordinate: %lld\n", yBuoundaryXcoordinate);
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// }
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}
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}
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}
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else
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{
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///return 0;
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if(i != (long long)(chain->length - 1)) zdrop_occ++;
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if(zdrop_occ > 1) return 0;
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sum_score += mapExtentScore;
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if(xRegionLen <= yRegionLen)
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{
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sum_score -= (GAP_OPEN_KSW + (xRegionLen - maxXpos)*GAP_EXT_KSW);
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}
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else
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{
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sum_score -= (GAP_OPEN_KSW + (yRegionLen - maxYpos)*GAP_EXT_KSW);
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}
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}
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}
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(*final_scores) = sum_score;
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if(new_xBeg != (long long)ovc->x_pos_s || new_xEnd != (long long)ovc->x_pos_e ||
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new_yBeg != (long long)ovc->y_pos_s || new_yEnd != (long long)ovc->y_pos_e)
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{
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// fprintf(stderr, "\ntttdirection: %u, new_xBeg: %lld, new_xEnd: %lld, new_yBeg: %lld, new_yEnd: %lld, old_xBeg: %u, old_xEnd: %u, old_yBeg: %u, old_yEnd: %u\n",
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// ovc->y_pos_strand, new_xBeg, new_xEnd, new_yBeg, new_yEnd, ovc->x_pos_s, ovc->x_pos_e, ovc->y_pos_s, ovc->y_pos_e);
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// fprintf(stderr, "x_readLen: %lld, y_readLen: %lld\n", x_readLen, y_readLen);
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// fprintf(stderr, "xID: %lld, yID: %lld\n", ovc->x_id, ovc->y_id);
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// for (i = 0; i < (long long)chain->length; i++)
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// {
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// fprintf(stderr,"i: %lld, x_pos: %d, offset: %d\n",
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// i, get_fake_gap_pos(chain, i), get_fake_gap_shift(chain, i));
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// }
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}
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else
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{
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// fprintf(stderr, "\nkkkdirection: %u, new_xBeg: %lld, new_xEnd: %lld, new_yBeg: %lld, new_yEnd: %lld, old_xBeg: %u, old_xEnd: %u, old_yBeg: %u, old_yEnd: %u\n",
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// ovc->y_pos_strand, new_xBeg, new_xEnd, new_yBeg, new_yEnd, ovc->x_pos_s, ovc->x_pos_e, ovc->y_pos_s, ovc->y_pos_e);
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// fprintf(stderr, "x_readLen: %lld, y_readLen: %lld\n", x_readLen, y_readLen);
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// fprintf(stderr, "xID: %lld, yID: %lld\n", ovc->x_id, ovc->y_id);
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// for (i = 0; i < (long long)chain->length; i++)
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// {
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// fprintf(stderr,"i: %lld, x_pos: %d, offset: %d\n",
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// i, get_fake_gap_pos(chain, i), get_fake_gap_shift(chain, i));
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// }
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}
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return 1;
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}
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int fill_chain_by_affine_gap(Fake_Cigar* chain, char* x_string, char* y_string, overlap_region* ovc,
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long long x_readLen, long long y_readLen, Cigar_record* cigar, uint8_t* c2n, uint8_t* x_num, uint8_t* y_num,
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long long* minus_score_thres, long long* final_scores)
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{
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long long i, xOffset, yOffset, xRegionLen, yRegionLen, /**bandLen,**/ maxXpos, maxYpos, zdroped;
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long long mapGlobalScore, mapExtentScore;
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long long xBuoundaryScore, xBuoundaryYcoordinate, yBuoundaryScore, yBuoundaryXcoordinate;
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///float band_rate = 0.08;
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int endbouns, mode;
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long long xBeg, yBeg;
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xBeg = ovc->x_pos_s;
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yBeg = ovc->y_pos_s;
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if(chain->length <= 0) return 0;
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long long sum_score = 0, current_ovlp = 0, zdrop_occ = 0;
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long long chain_num = (long long)chain->length - 1;
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///align forward
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for (i = 0; i < chain_num; i++)
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{
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xOffset = get_fake_gap_pos(chain, i);
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yOffset = (xOffset - xBeg) + yBeg + get_fake_gap_shift(chain, i);
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///last region
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///higher endbouns for middle regions
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endbouns = MATCH_SCORE_KSW;
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xRegionLen = get_fake_gap_pos(chain, i+1) - xOffset;
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yRegionLen = (get_fake_gap_pos(chain, i+1) + get_fake_gap_shift(chain, i+1)) -
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(get_fake_gap_pos(chain, i) + get_fake_gap_shift(chain, i));
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///last region
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if(i == chain_num - 1)
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{
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xRegionLen++;
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yRegionLen++;
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}
|
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|
||||
mode = KSW_EZ_SCORE_ONLY | KSW_EZ_APPROX_MAX | KSW_EZ_APPROX_DROP;
|
||||
|
||||
|
||||
if(minus_score_thres)
|
||||
{
|
||||
current_ovlp = MIN((xOffset - xBeg), (yOffset - yBeg));
|
||||
current_ovlp = current_ovlp*MATCH_SCORE_KSW;
|
||||
if(current_ovlp - sum_score > (*minus_score_thres))
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
if(xOffset < 0) xOffset = 0;
|
||||
if(yOffset < 0) yOffset = 0;
|
||||
if(xRegionLen < 0) xRegionLen = 0;
|
||||
if(yRegionLen < 0) yRegionLen = 0;
|
||||
|
||||
///do alignment forward
|
||||
///text is x, query is y
|
||||
afine_gap_alignment(x_string+xOffset, x_num, xRegionLen, y_string+yOffset, y_num, yRegionLen,
|
||||
c2n, FORWARD_KSW, MATCH_SCORE_KSW, MISMATCH_SCORE_KSW, GAP_OPEN_KSW, GAP_EXT_KSW,
|
||||
/**bandLen,**/BAND_KSW, Z_DROP_KSW, endbouns, &maxXpos, &maxYpos, &mapGlobalScore,
|
||||
&mapExtentScore, &xBuoundaryScore, &xBuoundaryYcoordinate,
|
||||
&yBuoundaryScore, &yBuoundaryXcoordinate, &zdroped, mode);
|
||||
|
||||
|
||||
if(!zdroped)
|
||||
{
|
||||
sum_score += mapGlobalScore;
|
||||
}
|
||||
else
|
||||
{
|
||||
///return 0;
|
||||
zdrop_occ++;
|
||||
///if(zdrop_occ > 1) return 0;
|
||||
sum_score += mapExtentScore;
|
||||
if(xRegionLen <= yRegionLen)
|
||||
{
|
||||
sum_score -= (GAP_OPEN_KSW + (xRegionLen - maxXpos)*GAP_EXT_KSW);
|
||||
}
|
||||
else
|
||||
{
|
||||
sum_score -= (GAP_OPEN_KSW + (yRegionLen - maxYpos)*GAP_EXT_KSW);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
(*final_scores) = sum_score;
|
||||
return 1;
|
||||
}
|
||||
|
||||
|
||||
|
||||
long long get_affine_gap_score(overlap_region* ovc, UC_Read* g_read, UC_Read* overlap_read, uint8_t* x_num,
|
||||
uint8_t* y_num, uint64_t EstimateXOlen, uint64_t EstimateYOlen)
|
||||
{
|
||||
char* x_string;
|
||||
char* y_string;
|
||||
uint64_t yStrand;
|
||||
long long minus_score_thres = (MAX(EstimateXOlen, EstimateYOlen)*HIGH_HET_ERROR_RATE*(MATCH_SCORE_KSW+(MAX(MISMATCH_SCORE_KSW,GAP_EXT_KSW))));
|
||||
long long total_score_thres = MAX(EstimateXOlen, EstimateYOlen)*MATCH_SCORE_KSW - minus_score_thres;
|
||||
|
||||
yStrand = ovc->y_pos_strand;
|
||||
|
||||
if(yStrand == 0)
|
||||
{
|
||||
recover_UC_Read(overlap_read, &R_INF, ovc->y_id);
|
||||
}
|
||||
else
|
||||
{
|
||||
recover_UC_Read_RC(overlap_read, &R_INF, ovc->y_id);
|
||||
}
|
||||
x_string = g_read->seq;
|
||||
y_string = overlap_read->seq;
|
||||
|
||||
long long sum;
|
||||
|
||||
if(fill_chain_by_affine_gap(&(ovc->f_cigar), x_string, y_string, ovc, Get_READ_LENGTH(R_INF, ovc->x_id),
|
||||
Get_READ_LENGTH(R_INF, ovc->y_id), NULL, seq_nt6_table, x_num, y_num, &minus_score_thres, &sum) == 0)
|
||||
{
|
||||
return 0;
|
||||
}
|
||||
|
||||
if(sum >= total_score_thres) return 1;
|
||||
return 0;
|
||||
}
|
||||
|
||||
void recalcate_high_het_overlap(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read)
|
||||
{
|
||||
long long j, k, i;
|
||||
int threshold;
|
||||
long long y_id;
|
||||
int y_strand;
|
||||
long long y_readLen;
|
||||
long long x_start;
|
||||
long long x_end;
|
||||
long long x_len;
|
||||
long long total_y_start;
|
||||
long long total_y_end;
|
||||
long long y_start;
|
||||
long long Window_Len;
|
||||
char* x_string;
|
||||
char* y_string;
|
||||
int end_site;
|
||||
unsigned int error;
|
||||
int real_y_start;
|
||||
long long overlap_length;
|
||||
int extra_begin, extra_end;
|
||||
long long o_len;
|
||||
kvec_t(uint8_t) x_num;
|
||||
kvec_t(uint8_t) y_num;
|
||||
kv_init(x_num);
|
||||
kv_init(y_num);
|
||||
|
||||
for (j = 0; j < (long long)overlap_list->length; j++)
|
||||
{
|
||||
|
||||
if(overlap_list->list[j].w_list_length == 0) continue;
|
||||
y_id = overlap_list->list[j].y_id;
|
||||
y_strand = overlap_list->list[j].y_pos_strand;
|
||||
y_readLen = Get_READ_LENGTH((*R_INF), y_id);
|
||||
|
||||
//i corresponding to each window of a overlap
|
||||
//utilize the the end pos of pre-window in backwards
|
||||
for (i = overlap_list->list[j].w_list_length - 1; i >= 0; i--)
|
||||
{
|
||||
///the first matched window
|
||||
if(overlap_list->list[j].w_list[i].y_end != -1)
|
||||
{
|
||||
///note!!! need notification
|
||||
///this is the actual end postion in ystring
|
||||
total_y_start = overlap_list->list[j].w_list[i].y_end
|
||||
- overlap_list->list[j].w_list[i].extra_begin + 1;
|
||||
|
||||
///k corresponding to all unmatched windows at the right side of overlap_list->list[j].w_list[i]
|
||||
///so k starts from i + 1, and end to the first matched window
|
||||
for (k = i + 1; k < (long long)overlap_list->list[j].w_list_length && overlap_list->list[j].w_list[k].y_end == -1; k++)
|
||||
{
|
||||
extra_begin = extra_end = 0;
|
||||
|
||||
///if y_start > y_readLen, direct terminate
|
||||
if (total_y_start >= y_readLen)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
///there is no problem for x
|
||||
x_start = overlap_list->list[j].w_list[k].x_start;
|
||||
x_end = overlap_list->list[j].w_list[k].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
///there are two potiential reasons for unmatched window:
|
||||
///1. this window has a large number of differences
|
||||
///2. DP does not start from the right offset
|
||||
threshold = double_error_threshold(overlap_list->list[j].w_list[k].error_threshold, x_len);
|
||||
|
||||
y_start = total_y_start;
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
if(!determine_overlap_region(threshold, y_start, y_id, Window_Len, R_INF,
|
||||
&extra_begin, &extra_end, &y_start, &o_len))
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
if(o_len + threshold < x_len)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM(y_string, Window_Len, x_string, x_len, threshold, &error);
|
||||
|
||||
///if error==-1, unmatched
|
||||
if (error!=(unsigned int)-1)
|
||||
{
|
||||
overlap_list->list[j].w_list[k].cigar.length = -1;
|
||||
overlap_list->list[j].w_list[k].y_start = y_start;
|
||||
overlap_list->list[j].w_list[k].y_end = y_start + end_site;
|
||||
overlap_list->list[j].w_list[k].error = (int)error;
|
||||
///note!!! need notification
|
||||
overlap_list->list[j].w_list[k].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[k].extra_end = extra_end;
|
||||
overlap_list->list[j].w_list[k].error_threshold = threshold;
|
||||
|
||||
overlap_list->list[j].align_length += x_len;
|
||||
}
|
||||
else
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
///note!!! need notification
|
||||
total_y_start = y_start + end_site - extra_begin + 1;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
//i corresponding to each window of a overlap
|
||||
//utilize the the start pos of next window in forward
|
||||
for (i = 0; i < (long long)overlap_list->list[j].w_list_length; i++)
|
||||
{
|
||||
///find the first matched window, which should not be the first window
|
||||
///the pre-window of this matched window must be unmatched
|
||||
if(overlap_list->list[j].w_list[i].y_end != -1 && i != 0 && overlap_list->list[j].w_list[i - 1].y_end == -1)
|
||||
{
|
||||
///check if the start pos of this matched window has been calculated
|
||||
if(overlap_list->list[j].w_list[i].cigar.length == -1)
|
||||
{
|
||||
///there is no problem for x
|
||||
x_start = overlap_list->list[j].w_list[i].x_start;
|
||||
x_end = overlap_list->list[j].w_list[i].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
/****************************may have bugs********************************/
|
||||
threshold = overlap_list->list[j].w_list[i].error_threshold;
|
||||
/****************************may have bugs********************************/
|
||||
/****************************may have bugs********************************/
|
||||
///should not adjust threshold, since this window can be matched by the old threshold
|
||||
///threshold = Adjust_Threshold(threshold, x_len);
|
||||
/****************************may have bugs********************************/
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
|
||||
///y_start is the real y_start
|
||||
y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
extra_begin = overlap_list->list[j].w_list[i].extra_begin;
|
||||
extra_end = overlap_list->list[j].w_list[i].extra_end;
|
||||
o_len = Window_Len - extra_end - extra_begin;
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path,
|
||||
overlap_list->list[j].w_list[i].error, overlap_list->list[j].w_list[i].y_end - y_start);
|
||||
|
||||
|
||||
///y_start has already been calculated
|
||||
if (error != (unsigned int)-1)
|
||||
{
|
||||
///this condition is always wrong
|
||||
///in best case, real_y_start = threshold, end_site = Window_Len - threshold - 1
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
if(fix_boundary(x_string, x_len, threshold, y_start, real_y_start,
|
||||
end_site, extra_begin, extra_end, y_id, Window_Len, R_INF, dumy,
|
||||
y_strand, error, &y_start, &real_y_start, &end_site, &extra_begin,
|
||||
&extra_end, &error))
|
||||
{
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
overlap_list->list[j].w_list[i].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[i].extra_end = extra_end;
|
||||
}
|
||||
}
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[i]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
///note!!! need notification
|
||||
real_y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[i].y_start = real_y_start;
|
||||
///I forget why don't reduce the extra_begin for y_end
|
||||
///it seems extra_begin will be reduced at the end of this function
|
||||
overlap_list->list[j].w_list[i].y_end = y_start + end_site;
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
}
|
||||
else
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
real_y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
}
|
||||
|
||||
|
||||
///the end pos for pre window is real_y_start - 1
|
||||
total_y_end = real_y_start - 1;
|
||||
///find the unmatched window on the left of current matched window
|
||||
///k starts from i - 1
|
||||
for (k = i - 1; k >= 0 && overlap_list->list[j].w_list[k].y_end == -1; k--)
|
||||
{
|
||||
///there is no problem in x
|
||||
x_start = overlap_list->list[j].w_list[k].x_start;
|
||||
x_end = overlap_list->list[j].w_list[k].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
///there are two potiential reasons for unmatched window:
|
||||
///1. this window has a large number of differences
|
||||
///2. DP does not start from the right offset
|
||||
threshold = double_error_threshold(overlap_list->list[j].w_list[k].error_threshold, x_len);
|
||||
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
if(total_y_end <= 0)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
///y_start might be less than 0
|
||||
y_start = total_y_end - x_len + 1;
|
||||
if(!determine_overlap_region(threshold, y_start, y_id, Window_Len, R_INF,
|
||||
&extra_begin, &extra_end, &y_start, &o_len))
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
if(o_len + threshold < x_len)
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path, -1, -1);
|
||||
|
||||
if (error!=(unsigned int)-1)
|
||||
{
|
||||
///this condition is always wrong
|
||||
///in best case, real_y_start = threshold, end_site = Window_Len - threshold - 1
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
fix_boundary(x_string, x_len, threshold, y_start, real_y_start, end_site,
|
||||
extra_begin, extra_end, y_id, Window_Len, R_INF, dumy, y_strand, error,
|
||||
&y_start, &real_y_start, &end_site,
|
||||
&extra_begin, &extra_end, &error);
|
||||
}
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[k]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
///y_start has no shift, but y_end has shift
|
||||
overlap_list->list[j].w_list[k].y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[k].y_end = y_start + end_site;
|
||||
overlap_list->list[j].w_list[k].error = error;
|
||||
overlap_list->list[j].align_length += x_len;
|
||||
overlap_list->list[j].w_list[k].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[k].extra_end = extra_end;
|
||||
overlap_list->list[j].w_list[k].error_threshold = threshold;
|
||||
}
|
||||
else
|
||||
{
|
||||
break;
|
||||
}
|
||||
|
||||
total_y_end = y_start + real_y_start - 1 - extra_begin;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
overlap_list->mapped_overlaps_length = 0;
|
||||
|
||||
double error_rate;
|
||||
int is_update = 0;
|
||||
for (j = 0; j < (long long)overlap_list->length; j++)
|
||||
{
|
||||
y_id = overlap_list->list[j].y_id;
|
||||
y_strand = overlap_list->list[j].y_pos_strand;
|
||||
y_readLen = Get_READ_LENGTH((*R_INF), y_id);
|
||||
overlap_length = overlap_list->list[j].x_pos_e - overlap_list->list[j].x_pos_s + 1;
|
||||
overlap_list->list[j].is_match = 0;
|
||||
is_update = 0;
|
||||
///debug_scan_cigar(&(overlap_list->list[j]));
|
||||
if(overlap_list->list[j].w_list_length == 0 || overlap_length == 0 || overlap_list->list[j].align_length == 0) continue;
|
||||
///only calculate cigar for high quality overlaps
|
||||
if (overlap_length * OVERLAP_THRESHOLD_FILTER <= overlap_list->list[j].align_length)
|
||||
{
|
||||
|
||||
for (i = 0; i < (long long)overlap_list->list[j].w_list_length; i++)
|
||||
{
|
||||
///first we need to check if this window is matched
|
||||
if(overlap_list->list[j].w_list[i].y_end != -1)
|
||||
{
|
||||
///second check if the cigar of this window has been got
|
||||
if(overlap_list->list[j].w_list[i].cigar.length == -1)
|
||||
{
|
||||
///there is no problem for x
|
||||
x_start = overlap_list->list[j].w_list[i].x_start;
|
||||
x_end = overlap_list->list[j].w_list[i].x_end;
|
||||
x_len = x_end - x_start + 1;
|
||||
/****************************may have bugs********************************/
|
||||
///threshold = x_len * asm_opt.max_ov_diff_ec;
|
||||
threshold = overlap_list->list[j].w_list[i].error_threshold;
|
||||
/****************************may have bugs********************************/
|
||||
/****************************may have bugs********************************/
|
||||
///should not adjust threshold, since this window can be matched by the old threshold
|
||||
///threshold = Adjust_Threshold(threshold, x_len);
|
||||
/****************************may have bugs********************************/
|
||||
Window_Len = x_len + (threshold << 1);
|
||||
|
||||
|
||||
///y_start is the real y_start
|
||||
///for the window with cigar, y_start has already reduced extra_begin
|
||||
y_start = overlap_list->list[j].w_list[i].y_start;
|
||||
extra_begin = overlap_list->list[j].w_list[i].extra_begin;
|
||||
extra_end = overlap_list->list[j].w_list[i].extra_end;
|
||||
o_len = Window_Len - extra_end - extra_begin;
|
||||
fill_subregion(dumy->overlap_region, y_start, o_len, y_strand,
|
||||
R_INF, y_id, extra_begin, extra_end);
|
||||
x_string = g_read->seq + x_start;
|
||||
y_string = dumy->overlap_region;
|
||||
|
||||
|
||||
///note!!! need notification
|
||||
end_site = Reserve_Banded_BPM_PATH(y_string, Window_Len, x_string, x_len, threshold, &error, &real_y_start,
|
||||
&(dumy->path_length), dumy->matrix_bit, dumy->path,
|
||||
overlap_list->list[j].w_list[i].error, overlap_list->list[j].w_list[i].y_end - y_start);
|
||||
|
||||
if (error != (unsigned int)-1)
|
||||
{
|
||||
if (end_site == Window_Len - 1 || real_y_start == 0)
|
||||
{
|
||||
|
||||
if(fix_boundary(x_string, x_len, threshold, y_start, real_y_start, end_site,
|
||||
extra_begin, extra_end, y_id, Window_Len, R_INF, dumy, y_strand, error,
|
||||
&y_start, &real_y_start, &end_site,
|
||||
&extra_begin, &extra_end, &error))
|
||||
{
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
overlap_list->list[j].w_list[i].extra_begin = extra_begin;
|
||||
overlap_list->list[j].w_list[i].extra_end = extra_end;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
generate_cigar(dumy->path, dumy->path_length, &(overlap_list->list[j].w_list[i]),
|
||||
&real_y_start, &end_site, &error, x_string, x_len, y_string);
|
||||
|
||||
///note!!! need notification
|
||||
real_y_start = y_start + real_y_start - extra_begin;
|
||||
overlap_list->list[j].w_list[i].y_start = real_y_start;
|
||||
overlap_list->list[j].w_list[i].y_end = y_start + end_site - extra_begin;
|
||||
overlap_list->list[j].w_list[i].error = error;
|
||||
}
|
||||
else
|
||||
{
|
||||
fprintf(stderr, "error\n");
|
||||
}
|
||||
}
|
||||
else
|
||||
{
|
||||
overlap_list->list[j].w_list[i].y_end -= overlap_list->list[j].w_list[i].extra_begin;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
error_rate = non_trim_error_rate(overlap_list, j, R_INF, dumy, g_read);
|
||||
|
||||
|
||||
if (error_rate <= HIGH_HET_ERROR_RATE)
|
||||
{
|
||||
is_update = 1;
|
||||
}
|
||||
}
|
||||
|
||||
if((is_update == 0) && (overlap_list->list[j].align_length >= WINDOW) &&
|
||||
(overlap_length * HIGH_HET_OVERLAP_THRESHOLD_FILTER <= overlap_list->list[j].align_length))
|
||||
{
|
||||
kv_resize(uint8_t, x_num, (uint64_t)(Get_READ_LENGTH((*R_INF), overlap_list->list[j].x_id)));
|
||||
kv_resize(uint8_t, y_num, (uint64_t)(Get_READ_LENGTH((*R_INF), overlap_list->list[j].y_id)));
|
||||
is_update = get_affine_gap_score(&(overlap_list->list[j]), g_read, overlap_read, x_num.a, y_num.a,
|
||||
overlap_list->list[j].x_pos_e + 1 - overlap_list->list[j].x_pos_s,
|
||||
overlap_list->list[j].y_pos_e + 1 - overlap_list->list[j].y_pos_s);
|
||||
}
|
||||
|
||||
if(is_update)
|
||||
{
|
||||
overlap_list->list[j].is_match = 2;
|
||||
}
|
||||
}
|
||||
|
||||
kv_destroy(x_num);
|
||||
kv_destroy(y_num);
|
||||
}
|
||||
|
||||
|
||||
|
||||
void correct_overlap_high_het(overlap_region_alloc* overlap_list, All_reads* R_INF,
|
||||
UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read)
|
||||
{
|
||||
clear_Correct_dumy(dumy, overlap_list);
|
||||
|
||||
long long window_start, window_end;
|
||||
|
||||
Window_Pool w_inf;
|
||||
|
||||
init_Window_Pool(&w_inf, g_read->length, WINDOW, (int)(1.0/asm_opt.max_ov_diff_ec));
|
||||
|
||||
int flag = 0;
|
||||
|
||||
while(get_Window(&w_inf, &window_start, &window_end) && flag != -2)
|
||||
{
|
||||
dumy->length = 0;
|
||||
dumy->lengthNT = 0;
|
||||
flag = get_interval(window_start, window_end, overlap_list, dumy);
|
||||
|
||||
switch (flag)
|
||||
{
|
||||
case 1: ///no match here
|
||||
break;
|
||||
case 0: ///no match here
|
||||
break;
|
||||
case -2: ///if flag == -2, loop would be terminated
|
||||
break;
|
||||
}
|
||||
|
||||
///dumy->lengthNT represent how many overlaps that the length of them is not equal to WINDOW; may larger or less than WINDOW
|
||||
///dumy->length represent how many overlaps that the length of them is WINDOW
|
||||
/****************************may improve**************************/
|
||||
///now the windows which are larger than WINDOW are verified one-by-one, to improve it, we can do it group-bygroup
|
||||
verify_window(window_start, window_end, overlap_list, dumy, R_INF, g_read->seq);
|
||||
}
|
||||
|
||||
recalcate_high_het_overlap(overlap_list, R_INF, g_read, dumy, overlap_read);
|
||||
}
|
||||
Reference in New Issue
Block a user