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r1183: added lr:hq; fixed transition

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* Added the lr:hq preset suggested by Nanopore developers (#1127)
 * Fixed transition scoring. It did not work with presets.
 * Cleaned up preset documentation
This commit is contained in:
Heng Li
2024-03-10 13:47:34 -04:00
parent bc588c0eeb
commit 8140259974
5 changed files with 73 additions and 29 deletions
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align.c
+9 -7
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@@ -23,13 +23,14 @@ static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc
static void ksw_gen_ts_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t transition, int8_t sc_ambi)
{
assert(m==5);
ksw_gen_simple_mat(m,mat,a,b,sc_ambi);
assert(m == 5);
ksw_gen_simple_mat(m, mat, a, b, sc_ambi);
if (transition == 0 || transition == b) return;
transition = transition > 0? -transition : transition;
mat[0*m+2]=transition; // A->G
mat[1*m+3]=transition; // C->T
mat[2*m+0]=transition; // G->A
mat[3*m+1]=transition; // T->C
mat[0 * m + 2] = transition; // A->G
mat[1 * m + 3] = transition; // C->T
mat[2 * m + 0] = transition; // G->A
mat[3 * m + 1] = transition; // T->C
}
static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
@@ -334,7 +335,8 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
for (i = 0; i < qlen; ++i) fputc("ACGTN"[qseq[i]], stderr);
fputc('\n', stderr);
}
if (opt->b != opt->transition) flag |= KSW_EZ_GENERIC_SC;
if (opt->transition != 0 && opt->b != opt->transition)
flag |= KSW_EZ_GENERIC_SC;
if (opt->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
ksw_reset_extz(ez);
ez->zdropped = 1;