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r1256: working for one example, but still buggy

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Heng Li
2025-04-06 10:33:57 -04:00
parent 1877818239
commit a8094ad859
6 changed files with 37 additions and 13 deletions
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30
jump.c
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@@ -1,3 +1,4 @@
#include <stdio.h>
#include "mmpriv.h"
#include "kalloc.h"
@@ -22,17 +23,26 @@ static int32_t mm_jump_check(void *km, const mm_idx_t *mi, int32_t qlen, const u
static uint8_t *mm_jump_get_qseq_seq(void *km, int32_t qlen, const uint8_t *qseq0, const mm_reg1_t *r, int32_t is_left, int32_t ql0, uint8_t *qseq)
{
int32_t i, k;
extern unsigned char seq_nt4_table[256];
int32_t i, k = 0;
if (!r->rev) {
if (is_left) memcpy(qseq, qseq0, ql0);
else memcpy(qseq, &qseq0[qlen - ql0], ql0);
if (is_left)
for (i = 0; i < ql0; ++i)
qseq[k++] = seq_nt4_table[(uint8_t)qseq0[i]];
else
for (i = qlen - ql0; i < qlen; ++i)
qseq[k++] = seq_nt4_table[(uint8_t)qseq0[i]];
} else {
if (is_left)
for (i = qlen - 1, k = 0; i >= qlen - ql0; --i)
qseq[k++] = qseq0[i] >= 4? qseq0[i] : 3 - qseq0[i];
for (i = qlen - 1; i >= qlen - ql0; --i) {
uint8_t c = seq_nt4_table[(uint8_t)qseq0[i]];
qseq[k++] = c >= 4? c : 3 - c;
}
else
for (i = ql0 - 1, k = 0; i >= 0; --i)
qseq[k++] = qseq0[i] >= 4? qseq0[i] : 3 - qseq0[i];
for (i = ql0 - 1; i >= 0; --i) {
uint8_t c = seq_nt4_table[(uint8_t)qseq0[i]];
qseq[k++] = c >= 4? c : 3 - c;
}
}
return qseq;
}
@@ -73,7 +83,7 @@ static void mm_jump_split_left(void *km, const mm_idx_t *mi, const mm_mapopt_t *
for (mm2 = 0; j < clip + ext; ++j)
if (qseq[j] != tseq[j] || qseq[j] > 3 || tseq[j] > 3)
++mm2;
if (mm1 == 0 && mm2 == 1)
if (mm1 == 0 && mm2 <= 1)
i0 = i, ++m; // i0 points to the rightmost i
}
kfree(km, tseq);
@@ -113,7 +123,7 @@ static void mm_jump_split_right(void *km, const mm_idx_t *mi, const mm_mapopt_t
for (i = 0; i < n; ++i) { // traverse possible jumps
const mm_idx_jjump1_t *ai = &a[i];
int32_t tlen, tl1, j, mm1, mm2;
assert(ai->off >= r->rs - extt && ai->off < r->rs + ext);
assert(ai->off >= r->re - ext && ai->off < r->re + extt);
if (ts_strand * ai->strand < 0) continue; // wrong strand
if (ai->off2 <= ai->off) continue; // wrong direction
if (ai->off2 + clip + ext > mi->seq[r->rid].len) continue; // not long enough
@@ -133,7 +143,7 @@ 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)
if (mm1 == 0 && mm2 <= 1)
i0 = i0 >= 0? i0 : i, ++m; // i0 points to the leftmost i
}
kfree(km, tseq);