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comparison PsiCLASS-1.0.2/samtools-0.1.19/bam_aux.c @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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-1:000000000000 0:903fc43d6227
1 #include <ctype.h>
2 #include "bam.h"
3 #include "khash.h"
4 typedef char *str_p;
5 KHASH_MAP_INIT_STR(s, int)
6 KHASH_MAP_INIT_STR(r2l, str_p)
7
8 void bam_aux_append(bam1_t *b, const char tag[2], char type, int len, uint8_t *data)
9 {
10 int ori_len = b->data_len;
11 b->data_len += 3 + len;
12 b->l_aux += 3 + len;
13 if (b->m_data < b->data_len) {
14 b->m_data = b->data_len;
15 kroundup32(b->m_data);
16 b->data = (uint8_t*)realloc(b->data, b->m_data);
17 }
18 b->data[ori_len] = tag[0]; b->data[ori_len + 1] = tag[1];
19 b->data[ori_len + 2] = type;
20 memcpy(b->data + ori_len + 3, data, len);
21 }
22
23 uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
24 {
25 return bam_aux_get(b, tag);
26 }
27
28 #define __skip_tag(s) do { \
29 int type = toupper(*(s)); \
30 ++(s); \
31 if (type == 'Z' || type == 'H') { while (*(s)) ++(s); ++(s); } \
32 else if (type == 'B') (s) += 5 + bam_aux_type2size(*(s)) * (*(int32_t*)((s)+1)); \
33 else (s) += bam_aux_type2size(type); \
34 } while(0)
35
36 uint8_t *bam_aux_get(const bam1_t *b, const char tag[2])
37 {
38 uint8_t *s;
39 int y = tag[0]<<8 | tag[1];
40 s = bam1_aux(b);
41 while (s < b->data + b->data_len) {
42 int x = (int)s[0]<<8 | s[1];
43 s += 2;
44 if (x == y) return s;
45 __skip_tag(s);
46 }
47 return 0;
48 }
49 // s MUST BE returned by bam_aux_get()
50 int bam_aux_del(bam1_t *b, uint8_t *s)
51 {
52 uint8_t *p, *aux;
53 aux = bam1_aux(b);
54 p = s - 2;
55 __skip_tag(s);
56 memmove(p, s, b->l_aux - (s - aux));
57 b->data_len -= s - p;
58 b->l_aux -= s - p;
59 return 0;
60 }
61
62 int bam_aux_drop_other(bam1_t *b, uint8_t *s)
63 {
64 if (s) {
65 uint8_t *p, *aux;
66 aux = bam1_aux(b);
67 p = s - 2;
68 __skip_tag(s);
69 memmove(aux, p, s - p);
70 b->data_len -= b->l_aux - (s - p);
71 b->l_aux = s - p;
72 } else {
73 b->data_len -= b->l_aux;
74 b->l_aux = 0;
75 }
76 return 0;
77 }
78
79 void bam_init_header_hash(bam_header_t *header)
80 {
81 if (header->hash == 0) {
82 int ret, i;
83 khiter_t iter;
84 khash_t(s) *h;
85 header->hash = h = kh_init(s);
86 for (i = 0; i < header->n_targets; ++i) {
87 iter = kh_put(s, h, header->target_name[i], &ret);
88 kh_value(h, iter) = i;
89 }
90 }
91 }
92
93 void bam_destroy_header_hash(bam_header_t *header)
94 {
95 if (header->hash)
96 kh_destroy(s, (khash_t(s)*)header->hash);
97 }
98
99 int32_t bam_get_tid(const bam_header_t *header, const char *seq_name)
100 {
101 khint_t k;
102 khash_t(s) *h = (khash_t(s)*)header->hash;
103 k = kh_get(s, h, seq_name);
104 return k == kh_end(h)? -1 : kh_value(h, k);
105 }
106
107 int bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *beg, int *end)
108 {
109 char *s;
110 int i, l, k, name_end;
111 khiter_t iter;
112 khash_t(s) *h;
113
114 bam_init_header_hash(header);
115 h = (khash_t(s)*)header->hash;
116
117 *ref_id = *beg = *end = -1;
118 name_end = l = strlen(str);
119 s = (char*)malloc(l+1);
120 // remove space
121 for (i = k = 0; i < l; ++i)
122 if (!isspace(str[i])) s[k++] = str[i];
123 s[k] = 0; l = k;
124 // determine the sequence name
125 for (i = l - 1; i >= 0; --i) if (s[i] == ':') break; // look for colon from the end
126 if (i >= 0) name_end = i;
127 if (name_end < l) { // check if this is really the end
128 int n_hyphen = 0;
129 for (i = name_end + 1; i < l; ++i) {
130 if (s[i] == '-') ++n_hyphen;
131 else if (!isdigit(s[i]) && s[i] != ',') break;
132 }
133 if (i < l || n_hyphen > 1) name_end = l; // malformated region string; then take str as the name
134 s[name_end] = 0;
135 iter = kh_get(s, h, s);
136 if (iter == kh_end(h)) { // cannot find the sequence name
137 iter = kh_get(s, h, str); // try str as the name
138 if (iter == kh_end(h)) {
139 if (bam_verbose >= 2) fprintf(stderr, "[%s] fail to determine the sequence name.\n", __func__);
140 free(s); return -1;
141 } else s[name_end] = ':', name_end = l;
142 }
143 } else iter = kh_get(s, h, str);
144 if (iter == kh_end(h)) {
145 free(s);
146 return -1;
147 }
148 *ref_id = kh_val(h, iter);
149 // parse the interval
150 if (name_end < l) {
151 for (i = k = name_end + 1; i < l; ++i)
152 if (s[i] != ',') s[k++] = s[i];
153 s[k] = 0;
154 *beg = atoi(s + name_end + 1);
155 for (i = name_end + 1; i != k; ++i) if (s[i] == '-') break;
156 *end = i < k? atoi(s + i + 1) : 1<<29;
157 if (*beg > 0) --*beg;
158 } else *beg = 0, *end = 1<<29;
159 free(s);
160 return *beg <= *end? 0 : -1;
161 }
162
163 int32_t bam_aux2i(const uint8_t *s)
164 {
165 int type;
166 if (s == 0) return 0;
167 type = *s++;
168 if (type == 'c') return (int32_t)*(int8_t*)s;
169 else if (type == 'C') return (int32_t)*(uint8_t*)s;
170 else if (type == 's') return (int32_t)*(int16_t*)s;
171 else if (type == 'S') return (int32_t)*(uint16_t*)s;
172 else if (type == 'i' || type == 'I') return *(int32_t*)s;
173 else return 0;
174 }
175
176 float bam_aux2f(const uint8_t *s)
177 {
178 int type;
179 type = *s++;
180 if (s == 0) return 0.0;
181 if (type == 'f') return *(float*)s;
182 else return 0.0;
183 }
184
185 double bam_aux2d(const uint8_t *s)
186 {
187 int type;
188 type = *s++;
189 if (s == 0) return 0.0;
190 if (type == 'd') return *(double*)s;
191 else return 0.0;
192 }
193
194 char bam_aux2A(const uint8_t *s)
195 {
196 int type;
197 type = *s++;
198 if (s == 0) return 0;
199 if (type == 'A') return *(char*)s;
200 else return 0;
201 }
202
203 char *bam_aux2Z(const uint8_t *s)
204 {
205 int type;
206 type = *s++;
207 if (s == 0) return 0;
208 if (type == 'Z' || type == 'H') return (char*)s;
209 else return 0;
210 }
211
212 #ifdef _WIN32
213 double drand48()
214 {
215 return (double)rand() / RAND_MAX;
216 }
217 #endif