Mercurial > repos > siyuan > prada
comparison pyPRADA_1.2/tools/samtools-0.1.16/sam.c @ 0:acc2ca1a3ba4
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author | siyuan |
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date | Thu, 20 Feb 2014 00:44:58 -0500 |
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-1:000000000000 | 0:acc2ca1a3ba4 |
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1 #include <string.h> | |
2 #include <unistd.h> | |
3 #include "faidx.h" | |
4 #include "sam.h" | |
5 | |
6 #define TYPE_BAM 1 | |
7 #define TYPE_READ 2 | |
8 | |
9 bam_header_t *bam_header_dup(const bam_header_t *h0) | |
10 { | |
11 bam_header_t *h; | |
12 int i; | |
13 h = bam_header_init(); | |
14 *h = *h0; | |
15 h->hash = h->dict = h->rg2lib = 0; | |
16 h->text = (char*)calloc(h->l_text + 1, 1); | |
17 memcpy(h->text, h0->text, h->l_text); | |
18 h->target_len = (uint32_t*)calloc(h->n_targets, 4); | |
19 h->target_name = (char**)calloc(h->n_targets, sizeof(void*)); | |
20 for (i = 0; i < h->n_targets; ++i) { | |
21 h->target_len[i] = h0->target_len[i]; | |
22 h->target_name[i] = strdup(h0->target_name[i]); | |
23 } | |
24 return h; | |
25 } | |
26 static void append_header_text(bam_header_t *header, char* text, int len) | |
27 { | |
28 int x = header->l_text + 1; | |
29 int y = header->l_text + len + 1; // 1 byte null | |
30 if (text == 0) return; | |
31 kroundup32(x); | |
32 kroundup32(y); | |
33 if (x < y) header->text = (char*)realloc(header->text, y); | |
34 strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here. | |
35 header->l_text += len; | |
36 header->text[header->l_text] = 0; | |
37 } | |
38 | |
39 samfile_t *samopen(const char *fn, const char *mode, const void *aux) | |
40 { | |
41 samfile_t *fp; | |
42 fp = (samfile_t*)calloc(1, sizeof(samfile_t)); | |
43 if (strchr(mode, 'r')) { // read | |
44 fp->type |= TYPE_READ; | |
45 if (strchr(mode, 'b')) { // binary | |
46 fp->type |= TYPE_BAM; | |
47 fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r"); | |
48 if (fp->x.bam == 0) goto open_err_ret; | |
49 fp->header = bam_header_read(fp->x.bam); | |
50 } else { // text | |
51 fp->x.tamr = sam_open(fn); | |
52 if (fp->x.tamr == 0) goto open_err_ret; | |
53 fp->header = sam_header_read(fp->x.tamr); | |
54 if (fp->header->n_targets == 0) { // no @SQ fields | |
55 if (aux) { // check if aux is present | |
56 bam_header_t *textheader = fp->header; | |
57 fp->header = sam_header_read2((const char*)aux); | |
58 if (fp->header == 0) goto open_err_ret; | |
59 append_header_text(fp->header, textheader->text, textheader->l_text); | |
60 bam_header_destroy(textheader); | |
61 } | |
62 if (fp->header->n_targets == 0 && bam_verbose >= 1) | |
63 fprintf(stderr, "[samopen] no @SQ lines in the header.\n"); | |
64 } else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets); | |
65 } | |
66 } else if (strchr(mode, 'w')) { // write | |
67 fp->header = bam_header_dup((const bam_header_t*)aux); | |
68 if (strchr(mode, 'b')) { // binary | |
69 char bmode[3]; | |
70 int i, compress_level = -1; | |
71 for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; | |
72 if (mode[i]) compress_level = mode[i] - '0'; | |
73 if (strchr(mode, 'u')) compress_level = 0; | |
74 bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0; | |
75 fp->type |= TYPE_BAM; | |
76 fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode); | |
77 if (fp->x.bam == 0) goto open_err_ret; | |
78 bam_header_write(fp->x.bam, fp->header); | |
79 } else { // text | |
80 // open file | |
81 fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout; | |
82 if (fp->x.tamr == 0) goto open_err_ret; | |
83 if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2; | |
84 else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2; | |
85 else fp->type |= BAM_OFDEC<<2; | |
86 // write header | |
87 if (strchr(mode, 'h')) { | |
88 int i; | |
89 bam_header_t *alt; | |
90 // parse the header text | |
91 alt = bam_header_init(); | |
92 alt->l_text = fp->header->l_text; alt->text = fp->header->text; | |
93 sam_header_parse(alt); | |
94 alt->l_text = 0; alt->text = 0; | |
95 // check if there are @SQ lines in the header | |
96 fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL | |
97 if (alt->n_targets) { // then write the header text without dumping ->target_{name,len} | |
98 if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1) | |
99 fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n"); | |
100 } else { // then dump ->target_{name,len} | |
101 for (i = 0; i < fp->header->n_targets; ++i) | |
102 fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]); | |
103 } | |
104 bam_header_destroy(alt); | |
105 } | |
106 } | |
107 } | |
108 return fp; | |
109 | |
110 open_err_ret: | |
111 free(fp); | |
112 return 0; | |
113 } | |
114 | |
115 void samclose(samfile_t *fp) | |
116 { | |
117 if (fp == 0) return; | |
118 if (fp->header) bam_header_destroy(fp->header); | |
119 if (fp->type & TYPE_BAM) bam_close(fp->x.bam); | |
120 else if (fp->type & TYPE_READ) sam_close(fp->x.tamr); | |
121 else fclose(fp->x.tamw); | |
122 free(fp); | |
123 } | |
124 | |
125 int samread(samfile_t *fp, bam1_t *b) | |
126 { | |
127 if (fp == 0 || !(fp->type & TYPE_READ)) return -1; // not open for reading | |
128 if (fp->type & TYPE_BAM) return bam_read1(fp->x.bam, b); | |
129 else return sam_read1(fp->x.tamr, fp->header, b); | |
130 } | |
131 | |
132 int samwrite(samfile_t *fp, const bam1_t *b) | |
133 { | |
134 if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing | |
135 if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b); | |
136 else { | |
137 char *s = bam_format1_core(fp->header, b, fp->type>>2&3); | |
138 int l = strlen(s); | |
139 fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw); | |
140 free(s); | |
141 return l + 1; | |
142 } | |
143 } | |
144 | |
145 int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data) | |
146 { | |
147 bam_plbuf_t *buf; | |
148 int ret; | |
149 bam1_t *b; | |
150 b = bam_init1(); | |
151 buf = bam_plbuf_init(func, func_data); | |
152 bam_plbuf_set_mask(buf, mask); | |
153 while ((ret = samread(fp, b)) >= 0) | |
154 bam_plbuf_push(b, buf); | |
155 bam_plbuf_push(0, buf); | |
156 bam_plbuf_destroy(buf); | |
157 bam_destroy1(b); | |
158 return 0; | |
159 } | |
160 | |
161 char *samfaipath(const char *fn_ref) | |
162 { | |
163 char *fn_list = 0; | |
164 if (fn_ref == 0) return 0; | |
165 fn_list = calloc(strlen(fn_ref) + 5, 1); | |
166 strcat(strcpy(fn_list, fn_ref), ".fai"); | |
167 if (access(fn_list, R_OK) == -1) { // fn_list is unreadable | |
168 if (access(fn_ref, R_OK) == -1) { | |
169 fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref); | |
170 } else { | |
171 if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n"); | |
172 if (fai_build(fn_ref) == -1) { | |
173 fprintf(stderr, "[samfaipath] fail to build FASTA index.\n"); | |
174 free(fn_list); fn_list = 0; | |
175 } | |
176 } | |
177 } | |
178 return fn_list; | |
179 } |