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Optional per-read scoring parameters (abpoa_para_t.read_abpt) #13

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Optional per-read scoring parameters (abpoa_para_t.read_abpt) #13

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ac35b4e
Optional per-read scoring parameters (abpoa_para_t.read_abpt)
glennhickey Sep 30, 2026
5c63e32
Merge per-read-params: optional per-read scoring parameters
glennhickey Oct 1, 2026
47361c5
Merge ai-optimization-per-read-params into main: optional per-read sc…
glennhickey Oct 4, 2026
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4 changes: 4 additions & 0 deletions include/abpoa.h
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,10 @@ typedef struct {
double min_freq; // for multiploid data
int verbose; // to control output msg
int batch_index; // index of current file in batch mode (for output header)
// optional per-read scoring, indexed by input order within one abpoa_msa() call: a non-NULL
// entry (an abpoa_para_t *) scores that read's alignment to the graph in place of this struct.
// Graph construction and output still use this one. Owned by the caller, never freed here.
void **read_abpt;

// char LogTable65536[65536];
// char bit_table16[65536];
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4 changes: 4 additions & 0 deletions src/abpoa.h
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Expand Up @@ -84,6 +84,10 @@ typedef struct {
double min_freq; // for multiploid data
int verbose; // to control output msg
int batch_index; // index of current file in batch mode (for output header)
// optional per-read scoring, indexed by input order within one abpoa_msa() call: a non-NULL
// entry (an abpoa_para_t *) scores that read's alignment to the graph in place of this struct.
// Graph construction and output still use this one. Owned by the caller, never freed here.
void **read_abpt;

// char LogTable65536[65536];
// char bit_table16[65536];
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13 changes: 8 additions & 5 deletions src/abpoa_align.c
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Expand Up @@ -151,6 +151,7 @@ abpoa_para_t *abpoa_init_para(void) {

abpt->verbose = ABPOA_NONE_VERBOSE;
abpt->batch_index = 0; // 0 means not in batch mode
abpt->read_abpt = NULL; // every read scored with this struct

// abpt->simd_flag = simd_check();

Expand Down Expand Up @@ -216,6 +217,7 @@ int abpoa_anchor_poa(abpoa_t *ab, abpoa_para_t *abpt, uint8_t **seqs, int **weig
// uint8_t *seq1;
for (_i = 0; _i < n_seq; ++_i) {
i = read_id_map[_i]; read_id = exist_n_seq + i; qlen = seq_lens[i]; whole_res.n_cigar = 0, whole_res.m_cigar = 0, whole_res.graph_cigar = 0;
abpoa_para_t *rabpt = (abpt->read_abpt && abpt->read_abpt[i]) ? (abpoa_para_t*)abpt->read_abpt[i] : abpt;
// fprintf(stderr, "seq: # %d\n", i);
if (abpt->verbose >= ABPOA_DEBUG_VERBOSE) fprintf(stderr, "seq: # %d\n", i);
// seq-to-graph alignment and add alignment within each split window
Expand Down Expand Up @@ -271,7 +273,7 @@ int abpoa_anchor_poa(abpoa_t *ab, abpoa_para_t *abpt, uint8_t **seqs, int **weig
if (abpt->verbose >= ABPOA_DEBUG_VERBOSE) fprintf(stderr, "\tanchor: t: %d (id: %d), q: %d\n", end_tpos, end_id, end_qpos);

res.graph_cigar = 0; res.n_cigar = 0;
abpoa_align_sequence_to_subgraph(ab, abpt, beg_id, end_id, qseq+beg_qpos, end_qpos-beg_qpos, &res);
abpoa_align_sequence_to_subgraph(ab, rabpt, beg_id, end_id, qseq+beg_qpos, end_qpos-beg_qpos, &res);
abpoa_push_whole_cigar(&whole_res.n_cigar, &whole_res.m_cigar, &whole_res.graph_cigar, res.n_cigar, res.graph_cigar);
if (res.n_cigar) free(res.graph_cigar);
// abpoa_add_subgraph_alignment(ab, abpt, beg_id, end_id, qseq+beg_qpos, end_qpos-beg_qpos, qpos_to_node_id+beg_qpos, res, read_id, tot_n_seq, 1);
Expand All @@ -292,7 +294,7 @@ int abpoa_anchor_poa(abpoa_t *ab, abpoa_para_t *abpt, uint8_t **seqs, int **weig

if (abpt->verbose >= ABPOA_DEBUG_VERBOSE) fprintf(stderr, "\tanchor: t: %d (id: %d), q: %d\n", end_tpos, end_id, end_qpos);
res.graph_cigar = 0; res.n_cigar = 0;
abpoa_align_sequence_to_subgraph(ab, abpt, beg_id, end_id, qseq+beg_qpos, end_qpos-beg_qpos, &res);
abpoa_align_sequence_to_subgraph(ab, rabpt, beg_id, end_id, qseq+beg_qpos, end_qpos-beg_qpos, &res);
abpoa_push_whole_cigar(&whole_res.n_cigar, &whole_res.m_cigar, &whole_res.graph_cigar, res.n_cigar, res.graph_cigar);
if (res.n_cigar) free(res.graph_cigar);

Expand All @@ -318,10 +320,11 @@ int abpoa_poa(abpoa_t *ab, abpoa_para_t *abpt, uint8_t **seqs, int **weights, in
// uint8_t *seq1;
for (i = 0; i < n_seq; ++i) {
qlen = seq_lens[i]; qseq = seqs[i]; weight = weights[i]; read_id = exist_n_seq + i;
abpoa_para_t *rabpt = (abpt->read_abpt && abpt->read_abpt[i]) ? (abpoa_para_t*)abpt->read_abpt[i] : abpt;
if (abpt->verbose >= ABPOA_DEBUG_VERBOSE) fprintf(stderr, "seq: # %d\n", i);
res.graph_cigar = 0; res.n_cigar = 0;
if (abpoa_align_sequence_to_graph(ab, abpt, qseq, qlen, &res) >= 0) {
if (abpt->amb_strand && (res.best_score < MIN_OF_TWO(qlen, ab->abg->node_n-2) * abpt->max_mat * .3333)) { // TODO .3333
if (abpoa_align_sequence_to_graph(ab, rabpt, qseq, qlen, &res) >= 0) {
if (abpt->amb_strand && (res.best_score < MIN_OF_TWO(qlen, ab->abg->node_n-2) * rabpt->max_mat * .3333)) { // TODO .3333
rc_qseq = (uint8_t*)_err_malloc(sizeof(uint8_t) * qlen);
for (j = 0; j < qlen; ++j) {
if (qseq[qlen-j-1] < 4) rc_qseq[j] = 3 - qseq[qlen-j-1];
Expand All @@ -332,7 +335,7 @@ int abpoa_poa(abpoa_t *ab, abpoa_para_t *abpt, uint8_t **seqs, int **weights, in
rc_weight[j] = weight[qlen-j-1];
}
abpoa_res_t rc_res; rc_res.n_cigar = 0, rc_res.graph_cigar = 0;
simd_abpoa_align_sequence_to_graph(ab, abpt, rc_qseq, qlen, &rc_res);
simd_abpoa_align_sequence_to_graph(ab, rabpt, rc_qseq, qlen, &rc_res);
if (rc_res.best_score > res.best_score) {
abpoa_res_copy(&res, &rc_res);
qseq = rc_qseq;
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