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r796: more debugging code

This commit is contained in:
Heng Li 2014-08-07 14:58:51 -04:00
parent d9dfab2ba2
commit a1a57d97be
3 changed files with 12 additions and 7 deletions
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8
bwamem.c
View File

@ -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];

9
intel_ext.cpp
View File

@ -1,3 +1,4 @@
#include <stdio.h>
#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);
}

2
main.c
View File

@ -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[]);