#include <assert.h>
+#include <ctype.h>
#include "bam.h"
#include "bam2bcf.h"
#include "ksort.h"
#include "kaln.h"
-#define INDEL_DEBUG
-
#define MINUS_CONST 0x10000000
#define INDEL_WINDOW_SIZE 50
-#define INDEL_BAD_SCORE 10000
static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
{
*_tpos = x;
return last_y;
}
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
// l is the relative gap length and l_run is the length of the homopolymer on the reference
static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
{
int q, qh;
q = bca->openQ + bca->extQ * (abs(l) - 1);
- qh = l_run >= 3? (int)(bca->tandemQ * (double)l / l_run + .499) : 1000;
+ qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
return q < qh? q : qh;
}
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+ int i, j, max = 0, max_i = pos, score = 0;
+ l = abs(l);
+ for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+ if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+ else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+ if (score < 0) break;
+ if (max < score) max = score, max_i = i;
+ }
+ return max_i - pos;
+}
+
int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref)
{
extern void ks_introsort_uint32_t(int, uint32_t*);
char *inscns = 0, *ref2, *query;
if (ref == 0 || bca == 0) return -1;
// determine if there is a gap
- for (s = 0; s < n; ++s) {
+ for (s = N = 0; s < n; ++s) {
+ N += n_plp[s]; // N is the total number of reads
for (i = 0; i < n_plp[s]; ++i)
if (plp[s][i].indel != 0) break;
if (i < n_plp[s]) break;
{ // find out how many types of indels are present
int m;
uint32_t *aux;
- aux = calloc(n + 1, 4);
+ aux = calloc(N + 1, 4);
m = max_rd_len = 0;
aux[m++] = MINUS_CONST; // zero indel is always a type
- for (s = N = 0; s < n; ++s) {
- N += n_plp[s]; // N is the total number of reads
+ for (s = 0; s < n; ++s) {
for (i = 0; i < n_plp[s]; ++i) {
const bam_pileup1_t *p = plp[s] + i;
if (p->indel != 0)
ref2 = calloc(right - left + max_ins + 2, 1);
query = calloc(right - left + max_rd_len + max_ins + 2, 1);
score = calloc(N * n_types, sizeof(int));
+ bca->indelreg = 0;
for (t = 0; t < n_types; ++t) {
- int l;
+ int l, ir;
ka_param2_t ap = ka_param2_qual;
ap.band_width = abs(types[t]) + 3;
+ // compute indelreg
+ if (types[t] == 0) ir = 0;
+ else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
+ else ir = est_indelreg(pos, ref, -types[t], 0);
+ if (ir > bca->indelreg) bca->indelreg = ir;
+// fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
// write ref2
for (k = 0, j = left; j <= pos; ++j)
ref2[k++] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[j]]];
// determine the start and end of sequences for alignment
qbeg = tpos2qpos(&p->b->core, bam1_cigar(p->b), left, 0, &tbeg);
qend = tpos2qpos(&p->b->core, bam1_cigar(p->b), right, 1, &tend);
- assert(tbeg >= left);
+ if (types[t] < 0) {
+ int l = -types[t];
+ tbeg = tbeg - l > left? tbeg - l : left;
+ }
// write the query sequence
for (l = qbeg; l < qend; ++l)
query[l - qbeg] = bam_nt16_nt4_table[bam1_seqi(seq, l)];
// do alignment; this takes most of computing time for indel calling
-#ifdef INDEL_DEBUG
- for (sc = 0; sc < tend - tbeg + types[t]; ++sc)
- fputc("ACGTN"[(int)ref2[tbeg-left+sc]], stderr);
- fputc('\n', stderr);
- for (sc = 0; sc < qend - qbeg; ++sc) fputc("ACGTN"[(int)query[qbeg + sc]], stderr);
- fputc('\n', stderr);
-#endif
sc = ka_global_score((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
(uint8_t*)query + qbeg, qend - qbeg, &ap);
-#ifdef INDEL_DEBUG
- fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
-#endif
score[K*n_types + t] = -sc;
+/*
+ for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+ fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+ fputc('\n', stderr);
+ for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[qbeg + l]], stderr);
+ fputc('\n', stderr);
+ fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s score=%d\n", pos, types[t], s, i, bam1_qname(p->b), sc);
+*/
}
}
}
free(ref2); free(query);
- { // choose the top 4 indel types; reference must be included
- }
{ // compute indelQ
int *sc, tmp, *sumq;
sc = alloca(n_types * sizeof(int));
tmp = est_seqQ(bca, types[sc[0]&0x3f], l_run);
}
if (indelQ > tmp) indelQ = tmp;
- if (indelQ > p->b->core.qual) indelQ = p->b->core.qual;
- if (indelQ > bca->capQ) indelQ = bca->capQ;
p->aux = (sc[0]&0x3f)<<8 | indelQ;
sumq[sc[0]&0x3f] += indelQ;
+// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ);
}
}
- // determine bca->indel_types[]
+ // determine bca->indel_types[] and bca->inscns
+ bca->maxins = max_ins;
+ bca->inscns = realloc(bca->inscns, bca->maxins * 4);
for (t = 0; t < n_types; ++t)
sumq[t] = sumq[t]<<6 | t;
for (t = 1; t < n_types; ++t) // insertion sort
sumq[0] = tmp;
}
for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
- for (t = 0; t < 4 && t < n_types; ++t)
+ for (t = 0; t < 4 && t < n_types; ++t) {
bca->indel_types[t] = types[sumq[t]&0x3f];
+ memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+ }
+ // update p->aux
+ for (s = K = 0; s < n; ++s) {
+ for (i = 0; i < n_plp[s]; ++i, ++K) {
+ bam_pileup1_t *p = plp[s] + i;
+ int x = types[p->aux>>8&0x3f];
+ for (j = 0; j < 4; ++j)
+ if (x == bca->indel_types[j]) break;
+ p->aux = j<<8 | (j == 4? 0 : (p->aux&0xff));
+// fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d q=%d\n", pos, s, i, bam1_qname(p->b), p->aux>>8&63, p->aux&0xff);
+ }
+ }
}
- // FIXME: to set the inserted sequence
free(score);
// free
free(types); free(inscns);
projects / samtools.git / blobdiff