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Illumina Complete Long Read presets (#1069)

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* Implements a transition-aware alignment scoring scheme and configuration presets for ICLR

* Fix to enable use of general scoring matrix in ksw as suggested by lh3

---------

Co-authored-by: koadman <>
This commit is contained in:
Aaron Darling
2023-06-04 11:06:15 -04:00
committed by GitHub
co-authored by koadman
parent e28a55be86
commit ace990c381
5 changed files with 32 additions and 6 deletions
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align.c
+14 -2
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@@ -21,6 +21,17 @@ static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc
mat[(m - 1) * m + j] = sc_ambi;
}
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);
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
}
static inline void mm_seq_rev(uint32_t len, uint8_t *seq)
{
uint32_t i;
@@ -323,6 +334,7 @@ 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->max_sw_mat > 0 && (int64_t)tlen * qlen > opt->max_sw_mat) {
ksw_reset_extz(ez);
ez->zdropped = 1;
@@ -586,7 +598,7 @@ static void mm_align1(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, int
r2->cnt = 0;
if (r->cnt == 0) return;
ksw_gen_simple_mat(5, mat, opt->a, opt->b, opt->sc_ambi);
ksw_gen_ts_mat(5, mat, opt->a, opt->b, opt->transition, opt->sc_ambi);
bw = (int)(opt->bw * 1.5 + 1.);
bw_long = (int)(opt->bw_long * 1.5 + 1.);
if (bw_long < bw) bw_long = bw;
@@ -844,7 +856,7 @@ static int mm_align1_inv(void *km, const mm_mapopt_t *opt, const mm_idx_t *mi, i
if (ql < opt->min_chain_score || ql > opt->max_gap) return 0;
if (tl < opt->min_chain_score || tl > opt->max_gap) return 0;
ksw_gen_simple_mat(5, mat, opt->a, opt->b, opt->sc_ambi);
ksw_gen_ts_mat(5, mat, opt->a, opt->b, opt->transition, opt->sc_ambi);
tseq = (uint8_t*)kmalloc(km, tl);
mm_idx_getseq(mi, r1->rid, r1->re, r2->rs, tseq);
qseq = r1->rev? &qseq0[0][r2->qe] : &qseq0[1][qlen - r2->qs];