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comparison SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c @ 0:74f5ea818cea

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author ryanmorin
date Wed, 12 Oct 2011 19:50:38 -0400
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-1:000000000000 0:74f5ea818cea
1 #include <stdio.h>
2 #include <unistd.h>
3 #include <assert.h>
4 #include <fcntl.h>
5 #include "bam.h"
6
7 #ifdef _USE_KNETFILE
8 #include "knetfile.h"
9 #endif
10
11 #ifndef PACKAGE_VERSION
12 #define PACKAGE_VERSION "0.1.6 (r453)"
13 #endif
14
15 int bam_taf2baf(int argc, char *argv[]);
16 int bam_pileup(int argc, char *argv[]);
17 int bam_merge(int argc, char *argv[]);
18 int bam_index(int argc, char *argv[]);
19 int bam_sort(int argc, char *argv[]);
20 int bam_tview_main(int argc, char *argv[]);
21 int bam_mating(int argc, char *argv[]);
22 int bam_rmdup(int argc, char *argv[]);
23 int bam_rmdupse(int argc, char *argv[]);
24 int bam_flagstat(int argc, char *argv[]);
25 int bam_fillmd(int argc, char *argv[]);
26
27 int main_samview(int argc, char *argv[]);
28 int main_import(int argc, char *argv[]);
29
30 int faidx_main(int argc, char *argv[]);
31 int glf3_view_main(int argc, char *argv[]);
32
33 int bam_tagview(int argc, char *argv[])
34 {
35 bamFile fp;
36 bam_header_t *header;
37 bam1_t *b;
38 char tag[2];
39 int ret;
40 if (argc < 3) {
41 fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
42 return 1;
43 }
44 fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
45 assert(fp);
46 header = bam_header_read(fp);
47 if (header == 0) {
48 fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
49 return 1;
50 }
51 tag[0] = argv[2][0]; tag[1] = argv[2][1];
52 b = (bam1_t*)calloc(1, sizeof(bam1_t));
53 while ((ret = bam_read1(fp, b)) >= 0) {
54 uint8_t *d = bam_aux_get(b, tag);
55 if (d) {
56 printf("%s\t%d\t", bam1_qname(b), b->core.flag);
57 if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
58 else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
59 else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
60 else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
61 else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
62 else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
63 else printf("\n");
64 }
65 }
66 if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
67 free(b->data); free(b);
68 bam_header_destroy(header);
69 bam_close(fp);
70 return 0;
71 }
72
73 static int usage()
74 {
75 fprintf(stderr, "\n");
76 fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
77 fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION);
78 fprintf(stderr, "Usage: samtools <command> [options]\n\n");
79 fprintf(stderr, "Command: view SAM<->BAM conversion\n");
80 fprintf(stderr, " sort sort alignment file\n");
81 fprintf(stderr, " pileup generate pileup output\n");
82 fprintf(stderr, " faidx index/extract FASTA\n");
83 #if _CURSES_LIB != 0
84 fprintf(stderr, " tview text alignment viewer\n");
85 #endif
86 fprintf(stderr, " index index alignment\n");
87 fprintf(stderr, " fixmate fix mate information\n");
88 fprintf(stderr, " glfview print GLFv3 file\n");
89 fprintf(stderr, " flagstat simple stats\n");
90 fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n");
91 fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n");
92 fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n");
93 fprintf(stderr, "\n");
94 return 1;
95 }
96
97 int main(int argc, char *argv[])
98 {
99 #ifdef _WIN32
100 setmode(fileno(stdout), O_BINARY);
101 setmode(fileno(stdin), O_BINARY);
102 #ifdef _USE_KNETFILE
103 knet_win32_init();
104 #endif
105 #endif
106 if (argc < 2) return usage();
107 if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
108 else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
109 else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
110 else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
111 else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
112 else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1);
113 else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
114 else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
115 else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
116 else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+1);
117 else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
118 else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
119 else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
120 else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
121 else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
122 #if _CURSES_LIB != 0
123 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
124 #endif
125 else {
126 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
127 return 1;
128 }
129 return 0;
130 }