From a1a57d97be0f40b4d156cfff10df4db25ccb2cd9 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Thu, 7 Aug 2014 14:58:51 -0400 Subject: [PATCH] r796: more debugging code --- bwamem.c | 8 ++++---- intel_ext.cpp | 9 +++++++-- main.c | 2 +- 3 files changed, 12 insertions(+), 7 deletions(-) diff --git a/bwamem.c b/bwamem.c index 87f4ed0..28f9593 100644 --- a/bwamem.c +++ b/bwamem.c @@ -682,6 +682,8 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac if (bwa_verbose >= 4) { printf("*** Left extension: prev_score=%d; score=%d; bandwidth=%d; max_off_diagonal_dist=%d\n", prev, a->score, aw[0], max_off[0]); fflush(stdout); } if (a->score == prev || max_off[0] < (aw[0]>>1) + (aw[0]>>2)) break; } + +end_left_extend: // check whether we prefer to reach the end of the query if (gscore <= 0 || gscore <= a->score - opt->pen_clip5) { // local extension a->qb = s->qbeg - qle, a->rb = s->rbeg - tle; @@ -690,8 +692,6 @@ void mem_chain2aln(const mem_opt_t *opt, const bntseq_t *bns, const uint8_t *pac a->qb = 0, a->rb = s->rbeg - gtle; a->truesc = gscore; } - -end_left_extend: free(qs); free(rs); } else a->score = a->truesc = s->len * opt->a, a->qb = 0, a->rb = s->rbeg; @@ -716,6 +716,8 @@ end_left_extend: if (bwa_verbose >= 4) { printf("*** Right extension: prev_score=%d; score=%d; bandwidth=%d; max_off_diagonal_dist=%d\n", prev, a->score, aw[1], max_off[1]); fflush(stdout); } if (a->score == prev || max_off[1] < (aw[1]>>1) + (aw[1]>>2)) break; } + +end_right_extend: // similar to the above if (gscore <= 0 || gscore <= a->score - opt->pen_clip3) { // local extension a->qe = qe + qle, a->re = rmax[0] + re + tle; @@ -726,8 +728,6 @@ end_left_extend: } } else a->qe = l_query, a->re = s->rbeg + s->len; if (bwa_verbose >= 4) printf("*** Added alignment region: [%d,%d) <=> [%ld,%ld); score=%d; {left,right}_bandwidth={%d,%d}\n", a->qb, a->qe, (long)a->rb, (long)a->re, a->score, aw[0], aw[1]); - -end_right_extend: // compute seedcov for (i = 0, a->seedcov = 0; i < c->n; ++i) { const mem_seed_t *t = &c->seeds[i]; diff --git a/intel_ext.cpp b/intel_ext.cpp index ae01c66..7c0a2d5 100644 --- a/intel_ext.cpp +++ b/intel_ext.cpp @@ -1,3 +1,4 @@ +#include #include "intel_ext.h" extern "C" { @@ -72,7 +73,11 @@ int intel_extend(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, con if (qlen >= INTEL_MIN_LEN && qlen <= INTEL_MAX_LEN && tlen >= INTEL_MIN_LEN && tlen <= INTEL_MAX_LEN) { int score, a = mat[0]; filter_and_extend(target, tlen, query, qlen, h0/a, !!(end_bonus > 0), zdrop/a, *qle, *tle, score); - *max_off = w; *gtle = *tle; *gscore = score; - return score * a; + *max_off = 0; *gtle = *tle; *gscore = score; + score *= a; + int score2 = score, qle2 = *qle, tle2 = *tle; + score = ksw_extend(qlen, query, tlen, target, m, mat, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off); + fprintf(stderr, "[%d,%d,%d] %d:%d; %d:%d; %d:%d\n", qlen, tlen, h0, score, score2, *qle, qle2, *tle, tle2); + return score; } else return ksw_extend(qlen, query, tlen, target, m, mat, gapo, gape, w, end_bonus, zdrop, h0, qle, tle, gtle, gscore, max_off); } diff --git a/main.c b/main.c index 07416b9..427beb1 100644 --- a/main.c +++ b/main.c @@ -4,7 +4,7 @@ #include "utils.h" #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.7.10-r795-dirty" +#define PACKAGE_VERSION "0.7.10-r796-dirty" #endif int bwa_fa2pac(int argc, char *argv[]);