Mercurial > repos > ryanmorin > nextgen_variant_identification
view SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c @ 7:351b3acadd17 default tip
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author | ryanmorin |
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date | Tue, 18 Oct 2011 18:33:15 -0400 |
parents | 74f5ea818cea |
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#include <stdio.h> #include <unistd.h> #include <assert.h> #include <fcntl.h> #include "bam.h" #ifdef _USE_KNETFILE #include "knetfile.h" #endif #ifndef PACKAGE_VERSION #define PACKAGE_VERSION "0.1.6 (r453)" #endif int bam_taf2baf(int argc, char *argv[]); int bam_pileup(int argc, char *argv[]); int bam_merge(int argc, char *argv[]); int bam_index(int argc, char *argv[]); int bam_sort(int argc, char *argv[]); int bam_tview_main(int argc, char *argv[]); int bam_mating(int argc, char *argv[]); int bam_rmdup(int argc, char *argv[]); int bam_rmdupse(int argc, char *argv[]); int bam_flagstat(int argc, char *argv[]); int bam_fillmd(int argc, char *argv[]); int main_samview(int argc, char *argv[]); int main_import(int argc, char *argv[]); int faidx_main(int argc, char *argv[]); int glf3_view_main(int argc, char *argv[]); int bam_tagview(int argc, char *argv[]) { bamFile fp; bam_header_t *header; bam1_t *b; char tag[2]; int ret; if (argc < 3) { fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n"); return 1; } fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r"); assert(fp); header = bam_header_read(fp); if (header == 0) { fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n"); return 1; } tag[0] = argv[2][0]; tag[1] = argv[2][1]; b = (bam1_t*)calloc(1, sizeof(bam1_t)); while ((ret = bam_read1(fp, b)) >= 0) { uint8_t *d = bam_aux_get(b, tag); if (d) { printf("%s\t%d\t", bam1_qname(b), b->core.flag); if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d)); else if (d[0] == 'f') printf("%f\n", bam_aux2f(d)); else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d)); else if (d[0] == 'A') printf("%c\n", bam_aux2A(d)); else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d)); else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d)); else printf("\n"); } } if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret); free(b->data); free(b); bam_header_destroy(header); bam_close(fp); return 0; } static int usage() { fprintf(stderr, "\n"); fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n"); fprintf(stderr, "Version: %s\n\n", PACKAGE_VERSION); fprintf(stderr, "Usage: samtools <command> [options]\n\n"); fprintf(stderr, "Command: view SAM<->BAM conversion\n"); fprintf(stderr, " sort sort alignment file\n"); fprintf(stderr, " pileup generate pileup output\n"); fprintf(stderr, " faidx index/extract FASTA\n"); #if _CURSES_LIB != 0 fprintf(stderr, " tview text alignment viewer\n"); #endif fprintf(stderr, " index index alignment\n"); fprintf(stderr, " fixmate fix mate information\n"); fprintf(stderr, " glfview print GLFv3 file\n"); fprintf(stderr, " flagstat simple stats\n"); fprintf(stderr, " calmd recalculate MD/NM tags and '=' bases\n"); fprintf(stderr, " merge merge sorted alignments (Picard recommended)\n"); fprintf(stderr, " rmdup remove PCR duplicates (Picard recommended)\n"); fprintf(stderr, "\n"); return 1; } int main(int argc, char *argv[]) { #ifdef _WIN32 setmode(fileno(stdout), O_BINARY); setmode(fileno(stdin), O_BINARY); #ifdef _USE_KNETFILE knet_win32_init(); #endif #endif if (argc < 2) return usage(); if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1); else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1); else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1); else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1); else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1); else if (strcmp(argv[1], "index") == 0) return bam_index(argc-1, argv+1); else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1); else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1); else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1); else if (strcmp(argv[1], "rmdupse") == 0) return bam_rmdupse(argc-1, argv+1); else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1); else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1); else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1); else if (strcmp(argv[1], "calmd") == 0) return bam_fillmd(argc-1, argv+1); else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1); #if _CURSES_LIB != 0 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1); #endif else { fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]); return 1; } return 0; }