Mercurial > repos > ryanmorin > nextgen_variant_identification
diff SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c @ 0:74f5ea818cea
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/bamtk.c Wed Oct 12 19:50:38 2011 -0400 @@ -0,0 +1,130 @@ +#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; +}