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#include "pysam.h"
#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include "bam.h"
#include "errmod.h"
#include "faidx.h"
#define ERR_DEP 0.83f
typedef struct {
int e[2][3], p[2][2];
} score_param_t;
/* Note that although the two matrics have 10 parameters in total, only 4
* (probably 3) are free. Changing the scoring matrices in a sort of symmetric
* way will not change the result. */
static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
typedef struct {
int min_baseQ, tid, max_bases;
uint16_t *bases;
bamFile fp;
bam_header_t *h;
char *ref;
faidx_t *fai;
errmod_t *em;
} ct_t;
static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
{
int i, j, ret, tmp, k, sum[4], qual;
float q[16];
if (n > g->max_bases) { // enlarge g->bases
g->max_bases = n;
kroundup32(g->max_bases);
g->bases = realloc(g->bases, g->max_bases * 2);
}
for (i = k = 0; i < n; ++i) {
const bam_pileup1_t *p = plp + i;
uint8_t *seq;
int q, baseQ, b;
if (p->is_refskip || p->is_del) continue;
baseQ = bam1_qual(p->b)[p->qpos];
if (baseQ < g->min_baseQ) continue;
seq = bam1_seq(p->b);
b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
if (b > 3) continue;
q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
if (q < 4) q = 4;
if (q > 63) q = 63;
g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b;
}
if (k == 0) return 0;
errmod_cal(g->em, k, 4, g->bases, q);
for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
for (i = 1; i < 4; ++i) // insertion sort
for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
qual = (sum[1]>>2) - (sum[0]>>2);
k = k < 256? k : 255;
ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
return ret<<8|k;
}
static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns)
{
int i, f[2][2], *prev, *curr, *swap_tmp, s;
uint8_t *b; // backtrack array
b = calloc(l, 1);
f[0][0] = f[0][1] = 0;
prev = f[0]; curr = f[1];
// fill the backtrack matrix
for (i = 0; i < l; ++i) {
int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
int tmp0, tmp1;
// compute f[0]
tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
else curr[0] = tmp1, b[i] = 1;
// compute f[1]
tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
else curr[1] = tmp1, b[i] |= 1<<1;
// swap
swap_tmp = prev; prev = curr; curr = swap_tmp;
}
// backtrack
s = prev[0] > prev[1]? 0 : 1;
for (i = l - 1; i > 0; --i) {
b[i] |= s<<2;
s = b[i]>>s&1;
}
// print
for (i = 0, s = -1; i <= l; ++i) {
if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
if (s >= 0) {
int j;
printf("%s:%d-%d\t0\t%s\t%d\t60\t%dM\t*\t0\t0\t", h->target_name[tid], s+1, i, h->target_name[tid], s+1, i-s);
for (j = s; j < i; ++j) {
int c = cns[j]>>8;
if (c == 0) putchar('N');
else putchar("ACGT"[c&3]);
}
putchar('\t');
for (j = s; j < i; ++j)
putchar(33 + (cns[j]>>8>>2));
putchar('\n');
}
//if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
s = -1;
} else if ((b[i]>>2&3) && s < 0) s = i;
}
free(b);
}
static int read_aln(void *data, bam1_t *b)
{
extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag);
ct_t *g = (ct_t*)data;
int ret, len;
ret = bam_read1(g->fp, b);
if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) {
if (b->core.tid != g->tid) { // then load the sequence
free(g->ref);
g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len);
g->tid = b->core.tid;
}
bam_prob_realn_core(b, g->ref, 1<<1|1);
}
return ret;
}
int main_cut_target(int argc, char *argv[])
{
int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
const bam_pileup1_t *p;
bam_plp_t plp;
uint16_t *cns;
ct_t g;
memset(&g, 0, sizeof(ct_t));
g.min_baseQ = 13; g.tid = -1;
while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) {
switch (c) {
case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
case '1': g_param.e[1][1] = atoi(optarg); break;
case '2': g_param.e[1][2] = atoi(optarg); break;
case 'f': g.fai = fai_load(optarg);
if (g.fai == 0) fprintf(pysamerr, "[%s] fail to load the fasta index.\n", __func__);
break;
}
}
if (argc == optind) {
fprintf(pysamerr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>\n");
return 1;
}
l = max_l = 0; cns = 0;
g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
g.h = bam_header_read(g.fp);
g.em = errmod_init(1 - ERR_DEP);
plp = bam_plp_init(read_aln, &g);
while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
if (tid < 0) break;
if (tid != lasttid) { // change of chromosome
if (cns) process_cns(g.h, lasttid, l, cns);
if (max_l < g.h->target_len[tid]) {
max_l = g.h->target_len[tid];
kroundup32(max_l);
cns = realloc(cns, max_l * 2);
}
l = g.h->target_len[tid];
memset(cns, 0, max_l * 2);
lasttid = tid;
}
cns[pos] = gencns(&g, n, p);
lastpos = pos;
}
process_cns(g.h, lasttid, l, cns);
free(cns);
bam_header_destroy(g.h);
bam_plp_destroy(plp);
bam_close(g.fp);
if (g.fai) {
fai_destroy(g.fai); free(g.ref);
}
errmod_destroy(g.em);
free(g.bases);
return 0;
}
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