|
0
|
1 #include <unistd.h>
|
|
|
2 #include <stdlib.h>
|
|
|
3 #include <string.h>
|
|
|
4 #include "bam.h"
|
|
|
5 #include "errmod.h"
|
|
|
6 #include "faidx.h"
|
|
|
7
|
|
|
8 #define ERR_DEP 0.83f
|
|
|
9
|
|
|
10 typedef struct {
|
|
|
11 int e[2][3], p[2][2];
|
|
|
12 } score_param_t;
|
|
|
13
|
|
|
14 /* Note that although the two matrics have 10 parameters in total, only 4
|
|
|
15 * (probably 3) are free. Changing the scoring matrices in a sort of symmetric
|
|
|
16 * way will not change the result. */
|
|
|
17 static score_param_t g_param = { {{0,0,0},{-4,1,6}}, {{0,-14000}, {0,0}} };
|
|
|
18
|
|
|
19 typedef struct {
|
|
|
20 int min_baseQ, tid, max_bases;
|
|
|
21 uint16_t *bases;
|
|
|
22 bamFile fp;
|
|
|
23 bam_header_t *h;
|
|
|
24 char *ref;
|
|
|
25 faidx_t *fai;
|
|
|
26 errmod_t *em;
|
|
|
27 } ct_t;
|
|
|
28
|
|
|
29 static uint16_t gencns(ct_t *g, int n, const bam_pileup1_t *plp)
|
|
|
30 {
|
|
|
31 int i, j, ret, tmp, k, sum[4], qual;
|
|
|
32 float q[16];
|
|
|
33 if (n > g->max_bases) { // enlarge g->bases
|
|
|
34 g->max_bases = n;
|
|
|
35 kroundup32(g->max_bases);
|
|
|
36 g->bases = realloc(g->bases, g->max_bases * 2);
|
|
|
37 }
|
|
|
38 for (i = k = 0; i < n; ++i) {
|
|
|
39 const bam_pileup1_t *p = plp + i;
|
|
|
40 uint8_t *seq;
|
|
|
41 int q, baseQ, b;
|
|
|
42 if (p->is_refskip || p->is_del) continue;
|
|
|
43 baseQ = bam1_qual(p->b)[p->qpos];
|
|
|
44 if (baseQ < g->min_baseQ) continue;
|
|
|
45 seq = bam1_seq(p->b);
|
|
|
46 b = bam_nt16_nt4_table[bam1_seqi(seq, p->qpos)];
|
|
|
47 if (b > 3) continue;
|
|
|
48 q = baseQ < p->b->core.qual? baseQ : p->b->core.qual;
|
|
|
49 if (q < 4) q = 4;
|
|
|
50 if (q > 63) q = 63;
|
|
|
51 g->bases[k++] = q<<5 | bam1_strand(p->b)<<4 | b;
|
|
|
52 }
|
|
|
53 if (k == 0) return 0;
|
|
|
54 errmod_cal(g->em, k, 4, g->bases, q);
|
|
|
55 for (i = 0; i < 4; ++i) sum[i] = (int)(q[i<<2|i] + .499) << 2 | i;
|
|
|
56 for (i = 1; i < 4; ++i) // insertion sort
|
|
|
57 for (j = i; j > 0 && sum[j] < sum[j-1]; --j)
|
|
|
58 tmp = sum[j], sum[j] = sum[j-1], sum[j-1] = tmp;
|
|
|
59 qual = (sum[1]>>2) - (sum[0]>>2);
|
|
|
60 k = k < 256? k : 255;
|
|
|
61 ret = (qual < 63? qual : 63) << 2 | (sum[0]&3);
|
|
|
62 return ret<<8|k;
|
|
|
63 }
|
|
|
64
|
|
|
65 static void process_cns(bam_header_t *h, int tid, int l, uint16_t *cns)
|
|
|
66 {
|
|
|
67 int i, f[2][2], *prev, *curr, *swap_tmp, s;
|
|
|
68 uint8_t *b; // backtrack array
|
|
|
69 b = calloc(l, 1);
|
|
|
70 f[0][0] = f[0][1] = 0;
|
|
|
71 prev = f[0]; curr = f[1];
|
|
|
72 // fill the backtrack matrix
|
|
|
73 for (i = 0; i < l; ++i) {
|
|
|
74 int c = (cns[i] == 0)? 0 : (cns[i]>>8 == 0)? 1 : 2;
|
|
|
75 int tmp0, tmp1;
|
|
|
76 // compute f[0]
|
|
|
77 tmp0 = prev[0] + g_param.e[0][c] + g_param.p[0][0]; // (s[i+1],s[i])=(0,0)
|
|
|
78 tmp1 = prev[1] + g_param.e[0][c] + g_param.p[1][0]; // (0,1)
|
|
|
79 if (tmp0 > tmp1) curr[0] = tmp0, b[i] = 0;
|
|
|
80 else curr[0] = tmp1, b[i] = 1;
|
|
|
81 // compute f[1]
|
|
|
82 tmp0 = prev[0] + g_param.e[1][c] + g_param.p[0][1]; // (s[i+1],s[i])=(1,0)
|
|
|
83 tmp1 = prev[1] + g_param.e[1][c] + g_param.p[1][1]; // (1,1)
|
|
|
84 if (tmp0 > tmp1) curr[1] = tmp0, b[i] |= 0<<1;
|
|
|
85 else curr[1] = tmp1, b[i] |= 1<<1;
|
|
|
86 // swap
|
|
|
87 swap_tmp = prev; prev = curr; curr = swap_tmp;
|
|
|
88 }
|
|
|
89 // backtrack
|
|
|
90 s = prev[0] > prev[1]? 0 : 1;
|
|
|
91 for (i = l - 1; i > 0; --i) {
|
|
|
92 b[i] |= s<<2;
|
|
|
93 s = b[i]>>s&1;
|
|
|
94 }
|
|
|
95 // print
|
|
|
96 for (i = 0, s = -1; i <= l; ++i) {
|
|
|
97 if (i == l || ((b[i]>>2&3) == 0 && s >= 0)) {
|
|
|
98 if (s >= 0) {
|
|
|
99 int j;
|
|
|
100 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);
|
|
|
101 for (j = s; j < i; ++j) {
|
|
|
102 int c = cns[j]>>8;
|
|
|
103 if (c == 0) putchar('N');
|
|
|
104 else putchar("ACGT"[c&3]);
|
|
|
105 }
|
|
|
106 putchar('\t');
|
|
|
107 for (j = s; j < i; ++j)
|
|
|
108 putchar(33 + (cns[j]>>8>>2));
|
|
|
109 putchar('\n');
|
|
|
110 }
|
|
|
111 //if (s >= 0) printf("%s\t%d\t%d\t%d\n", h->target_name[tid], s, i, i - s);
|
|
|
112 s = -1;
|
|
|
113 } else if ((b[i]>>2&3) && s < 0) s = i;
|
|
|
114 }
|
|
|
115 free(b);
|
|
|
116 }
|
|
|
117
|
|
|
118 static int read_aln(void *data, bam1_t *b)
|
|
|
119 {
|
|
|
120 extern int bam_prob_realn_core(bam1_t *b, const char *ref, int flag);
|
|
|
121 ct_t *g = (ct_t*)data;
|
|
|
122 int ret, len;
|
|
|
123 ret = bam_read1(g->fp, b);
|
|
|
124 if (ret >= 0 && g->fai && b->core.tid >= 0 && (b->core.flag&4) == 0) {
|
|
|
125 if (b->core.tid != g->tid) { // then load the sequence
|
|
|
126 free(g->ref);
|
|
|
127 g->ref = fai_fetch(g->fai, g->h->target_name[b->core.tid], &len);
|
|
|
128 g->tid = b->core.tid;
|
|
|
129 }
|
|
|
130 bam_prob_realn_core(b, g->ref, 1<<1|1);
|
|
|
131 }
|
|
|
132 return ret;
|
|
|
133 }
|
|
|
134
|
|
|
135 int main_cut_target(int argc, char *argv[])
|
|
|
136 {
|
|
|
137 int c, tid, pos, n, lasttid = -1, lastpos = -1, l, max_l;
|
|
|
138 const bam_pileup1_t *p;
|
|
|
139 bam_plp_t plp;
|
|
|
140 uint16_t *cns;
|
|
|
141 ct_t g;
|
|
|
142
|
|
|
143 memset(&g, 0, sizeof(ct_t));
|
|
|
144 g.min_baseQ = 13; g.tid = -1;
|
|
|
145 while ((c = getopt(argc, argv, "f:Q:i:o:0:1:2:")) >= 0) {
|
|
|
146 switch (c) {
|
|
|
147 case 'Q': g.min_baseQ = atoi(optarg); break; // quality cutoff
|
|
|
148 case 'i': g_param.p[0][1] = -atoi(optarg); break; // 0->1 transition (in) PENALTY
|
|
|
149 case '0': g_param.e[1][0] = atoi(optarg); break; // emission SCORE
|
|
|
150 case '1': g_param.e[1][1] = atoi(optarg); break;
|
|
|
151 case '2': g_param.e[1][2] = atoi(optarg); break;
|
|
|
152 case 'f': g.fai = fai_load(optarg);
|
|
|
153 if (g.fai == 0) fprintf(stderr, "[%s] fail to load the fasta index.\n", __func__);
|
|
|
154 break;
|
|
|
155 }
|
|
|
156 }
|
|
|
157 if (argc == optind) {
|
|
|
158 fprintf(stderr, "Usage: samtools targetcut [-Q minQ] [-i inPen] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>\n");
|
|
|
159 return 1;
|
|
|
160 }
|
|
|
161 l = max_l = 0; cns = 0;
|
|
|
162 g.fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "r") : bam_dopen(fileno(stdin), "r");
|
|
|
163 g.h = bam_header_read(g.fp);
|
|
|
164 g.em = errmod_init(1 - ERR_DEP);
|
|
|
165 plp = bam_plp_init(read_aln, &g);
|
|
|
166 while ((p = bam_plp_auto(plp, &tid, &pos, &n)) != 0) {
|
|
|
167 if (tid < 0) break;
|
|
|
168 if (tid != lasttid) { // change of chromosome
|
|
|
169 if (cns) process_cns(g.h, lasttid, l, cns);
|
|
|
170 if (max_l < g.h->target_len[tid]) {
|
|
|
171 max_l = g.h->target_len[tid];
|
|
|
172 kroundup32(max_l);
|
|
|
173 cns = realloc(cns, max_l * 2);
|
|
|
174 }
|
|
|
175 l = g.h->target_len[tid];
|
|
|
176 memset(cns, 0, max_l * 2);
|
|
|
177 lasttid = tid;
|
|
|
178 }
|
|
|
179 cns[pos] = gencns(&g, n, p);
|
|
|
180 lastpos = pos;
|
|
|
181 }
|
|
|
182 process_cns(g.h, lasttid, l, cns);
|
|
|
183 free(cns);
|
|
|
184 bam_header_destroy(g.h);
|
|
|
185 bam_plp_destroy(plp);
|
|
|
186 bam_close(g.fp);
|
|
|
187 if (g.fai) {
|
|
|
188 fai_destroy(g.fai); free(g.ref);
|
|
|
189 }
|
|
|
190 errmod_destroy(g.em);
|
|
|
191 free(g.bases);
|
|
|
192 return 0;
|
|
|
193 }
|
