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view SNV/SNVMix2_source/SNVMix2-v0.12.1-rc1/samtools-0.1.6/sam_view.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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#include <stdlib.h> #include <string.h> #include <stdio.h> #include <unistd.h> #include "sam.h" #include "faidx.h" static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0; static char *g_library, *g_rg; static inline int __g_skip_aln(const bam_header_t *h, const bam1_t *b) { if (b->core.qual < g_min_mapQ || ((b->core.flag & g_flag_on) != g_flag_on) || (b->core.flag & g_flag_off)) return 1; if (g_library || g_rg) { uint8_t *s = bam_aux_get(b, "RG"); if (s) { if (g_rg && strcmp(g_rg, (char*)(s + 1)) == 0) return 0; if (g_library) { const char *p = bam_strmap_get(h->rg2lib, (char*)(s + 1)); return (p && strcmp(p, g_library) == 0)? 0 : 1; } return 1; } else return 1; } else return 0; } // callback function for bam_fetch() static int view_func(const bam1_t *b, void *data) { if (!__g_skip_aln(((samfile_t*)data)->header, b)) samwrite((samfile_t*)data, b); return 0; } static int usage(int is_long_help); int main_samview(int argc, char *argv[]) { int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0; int of_type = BAM_OFDEC, is_long_help = 0; samfile_t *in = 0, *out = 0; char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0, *fn_ref = 0; /* parse command-line options */ strcpy(in_mode, "r"); strcpy(out_mode, "w"); while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:xX?T:")) >= 0) { switch (c) { case 'S': is_bamin = 0; break; case 'b': is_bamout = 1; break; case 't': fn_list = strdup(optarg); is_bamin = 0; break; case 'h': is_header = 1; break; case 'H': is_header_only = 1; break; case 'o': fn_out = strdup(optarg); break; case 'f': g_flag_on = strtol(optarg, 0, 0); break; case 'F': g_flag_off = strtol(optarg, 0, 0); break; case 'q': g_min_mapQ = atoi(optarg); break; case 'u': is_uncompressed = 1; break; case 'l': g_library = strdup(optarg); break; case 'r': g_rg = strdup(optarg); break; case 'x': of_type = BAM_OFHEX; break; case 'X': of_type = BAM_OFSTR; break; case '?': is_long_help = 1; break; case 'T': fn_ref = strdup(optarg); is_bamin = 0; break; default: return usage(is_long_help); } } if (is_uncompressed) is_bamout = 1; if (is_header_only) is_header = 1; if (is_bamout) strcat(out_mode, "b"); else { if (of_type == BAM_OFHEX) strcat(out_mode, "x"); else if (of_type == BAM_OFSTR) strcat(out_mode, "X"); } if (is_bamin) strcat(in_mode, "b"); if (is_header) strcat(out_mode, "h"); if (is_uncompressed) strcat(out_mode, "u"); if (argc == optind) return usage(is_long_help); // generate the fn_list if necessary if (fn_list == 0 && fn_ref) fn_list = samfaipath(fn_ref); // open file handlers if ((in = samopen(argv[optind], in_mode, fn_list)) == 0) { fprintf(stderr, "[main_samview] fail to open file for reading.\n"); goto view_end; } if (in->header == 0) { fprintf(stderr, "[main_samview] fail to read the header.\n"); goto view_end; } if ((out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) { fprintf(stderr, "[main_samview] fail to open file for writing.\n"); goto view_end; } if (is_header_only) goto view_end; // no need to print alignments if (argc == optind + 1) { // convert/print the entire file bam1_t *b = bam_init1(); int r; while ((r = samread(in, b)) >= 0) // read one alignment from `in' if (!__g_skip_aln(in->header, b)) samwrite(out, b); // write the alignment to `out' if (r < -1) fprintf(stderr, "[main_samview] truncated file.\n"); bam_destroy1(b); } else { // retrieve alignments in specified regions int i; bam_index_t *idx = 0; if (is_bamin) idx = bam_index_load(argv[optind]); // load BAM index if (idx == 0) { // index is unavailable fprintf(stderr, "[main_samview] random alignment retrieval only works for indexed BAM files.\n"); ret = 1; goto view_end; } for (i = optind + 1; i < argc; ++i) { int tid, beg, end; bam_parse_region(in->header, argv[i], &tid, &beg, &end); // parse a region in the format like `chr2:100-200' if (tid < 0) { // reference name is not found fprintf(stderr, "[main_samview] fail to get the reference name. Continue anyway.\n"); continue; } bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); // fetch alignments } bam_index_destroy(idx); // destroy the BAM index } view_end: // close files, free and return free(fn_list); free(fn_ref); free(fn_out); free(g_library); free(g_rg); samclose(in); samclose(out); return ret; } static int usage(int is_long_help) { fprintf(stderr, "\n"); fprintf(stderr, "Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]\n\n"); fprintf(stderr, "Options: -b output BAM\n"); fprintf(stderr, " -h print header for the SAM output\n"); fprintf(stderr, " -H print header only (no alignments)\n"); fprintf(stderr, " -S input is SAM\n"); fprintf(stderr, " -u uncompressed BAM output (force -b)\n"); fprintf(stderr, " -x output FLAG in HEX (samtools-C specific)\n"); fprintf(stderr, " -X output FLAG in string (samtools-C specific)\n"); fprintf(stderr, " -t FILE list of reference names and lengths (force -S) [null]\n"); fprintf(stderr, " -T FILE reference sequence file (force -S) [null]\n"); fprintf(stderr, " -o FILE output file name [stdout]\n"); fprintf(stderr, " -f INT required flag, 0 for unset [0]\n"); fprintf(stderr, " -F INT filtering flag, 0 for unset [0]\n"); fprintf(stderr, " -q INT minimum mapping quality [0]\n"); fprintf(stderr, " -l STR only output reads in library STR [null]\n"); fprintf(stderr, " -r STR only output reads in read group STR [null]\n"); fprintf(stderr, " -? longer help\n"); fprintf(stderr, "\n"); if (is_long_help) fprintf(stderr, "Notes:\n\ \n\ 1. By default, this command assumes the file on the command line is in\n\ the BAM format and it prints the alignments in SAM. If `-t' is\n\ applied, the input file is assumed to be in the SAM format. The\n\ file supplied with `-t' is SPACE/TAB delimited with the first two\n\ fields of each line consisting of the reference name and the\n\ corresponding sequence length. The `.fai' file generated by `faidx'\n\ can be used here. This file may be empty if reads are unaligned.\n\ \n\ 2. SAM->BAM conversion: `samtools view -bT ref.fa in.sam.gz'.\n\ \n\ 3. BAM->SAM conversion: `samtools view in.bam'.\n\ \n\ 4. A region should be presented in one of the following formats:\n\ `chr1', `chr2:1,000' and `chr3:1000-2,000'. When a region is\n\ specified, the input alignment file must be an indexed BAM file.\n\ \n\ 5. Option `-u' is preferred over `-b' when the output is piped to\n\ another samtools command.\n\ \n\ 6. In a string FLAG, each character represents one bit with\n\ p=0x1 (paired), P=0x2 (properly paired), u=0x4 (unmapped),\n\ U=0x8 (mate unmapped), r=0x10 (reverse), R=0x20 (mate reverse)\n\ 1=0x40 (first), 2=0x80 (second), s=0x100 (not primary), \n\ f=0x200 (failure) and d=0x400 (duplicate). Note that `-x' and\n\ `-X' are samtools-C specific. Picard and older samtools do not\n\ support HEX or string flags.\n\ \n"); return 1; } int main_import(int argc, char *argv[]) { int argc2, ret; char **argv2; if (argc != 4) { fprintf(stderr, "Usage: bamtk import <in.ref_list> <in.sam> <out.bam>\n"); return 1; } argc2 = 6; argv2 = calloc(6, sizeof(char*)); argv2[0] = "import", argv2[1] = "-o", argv2[2] = argv[3], argv2[3] = "-bt", argv2[4] = argv[1], argv2[5] = argv[2]; ret = main_samview(argc2, argv2); free(argv2); return ret; }