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r1258: update blen, mlen and dp_max0

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Heng Li
2025-04-06 15:26:01 -04:00
parent 2ed264db4e
commit dbc12b2838
2 changed files with 12 additions and 6 deletions
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jump.c
+11 -5
View File
@@ -50,7 +50,7 @@ static uint8_t *mm_jump_get_qseq_seq(void *km, int32_t qlen, const uint8_t *qseq
static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq0, mm_reg1_t *r, int32_t ts_strand)
{
uint8_t *tseq = 0, *qseq = 0;
int32_t i, n, i0 = -1, m = 0, l;
int32_t i, n, i0 = -1, m = 0, mm0 = 0, l;
int32_t ext = 1 + (opt->b + opt->a - 1) / opt->a + 1;
int32_t clip = !r->rev? r->qs : qlen - r->qe;
int32_t extt = clip < ext? clip : ext;
@@ -84,7 +84,7 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
++mm2;
if (mm1 == 0 && mm2 <= 1)
i0 = i, ++m; // i0 points to the rightmost i
i0 = i, mm0 = mm1 + mm2, ++m; // i0 points to the rightmost i
}
kfree(km, tseq);
@@ -99,6 +99,8 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
r->rs = a[i0].off2 - (clip + l);
if (!r->rev) r->qs = 0;
else r->qe = qlen;
r->blen += clip, r->mlen += clip - mm0;
r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
} else if (m > 0 && a[i0].off > r->rs) { // trim by l; l is always positive
r->p->cigar[0] -= l << 4 | MM_CIGAR_MATCH;
r->rs += l;
@@ -110,7 +112,7 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t *opt, int32_t qlen, const uint8_t *qseq0, mm_reg1_t *r, int32_t ts_strand)
{
uint8_t *tseq = 0, *qseq = 0;
int32_t i, n, i0 = -1, m = 0, l;
int32_t i, n, i0 = -1, m = 0, mm0 = 0, l;
int32_t ext = 1 + (opt->b + opt->a - 1) / opt->a + 1;
int32_t clip = !r->rev? qlen - r->qe : r->qs;
int32_t extt = clip < ext? clip : ext;
@@ -143,8 +145,10 @@ static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t
for (mm1 = 0; j < clip + ext; ++j)
if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
++mm1;
if (mm1 == 0 && mm2 <= 1)
i0 = i0 >= 0? i0 : i, ++m; // i0 points to the leftmost i
if (mm1 == 0 && mm2 <= 1) {
if (i0 < 0) i0 = i, mm0 = mm1 + mm2;
++m;
}
}
kfree(km, tseq);
@@ -159,6 +163,8 @@ static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t
r->re = a[i0].off2 + (clip + l);
if (!r->rev) r->qe = qlen;
else r->qs = 0;
r->blen += clip, r->mlen += clip - mm0;
r->p->dp_max0 += (clip - mm0) * opt->a - mm0 * opt->b;
} else if (m > 0 && r->re > a[i0].off) { // trim by l; l is always positive
r->p->cigar[r->p->n_cigar - 1] -= l << 4 | MM_CIGAR_MATCH;
r->re -= l;
minimap.h
+1 -1
View File
@@ -5,7 +5,7 @@
#include <stdio.h>
#include <sys/types.h>
#define MM_VERSION "2.28-r1257-dirty"
#define MM_VERSION "2.28-r1258-dirty"
#define MM_F_NO_DIAG (0x001LL) // no exact diagonal hit
#define MM_F_NO_DUAL (0x002LL) // skip pairs where query name is lexicographically larger than target name