X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fsam_view.c;fp=samtools%2Fsam_view.c;h=0000000000000000000000000000000000000000;hp=3b10e2e5372e98a2b9ebda4bd5791dc1b837a20f;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a diff --git a/samtools/sam_view.c b/samtools/sam_view.c deleted file mode 100644 index 3b10e2e..0000000 --- a/samtools/sam_view.c +++ /dev/null @@ -1,255 +0,0 @@ -#include -#include -#include -#include -#include -#include "sam_header.h" -#include "sam.h" -#include "faidx.h" -#include "khash.h" -KHASH_SET_INIT_STR(rg) - -typedef khash_t(rg) *rghash_t; - -rghash_t g_rghash = 0; -static int g_min_mapQ = 0, g_flag_on = 0, g_flag_off = 0; -static char *g_library, *g_rg; -static int g_sol2sanger_tbl[128]; - -static void sol2sanger(bam1_t *b) -{ - int l; - uint8_t *qual = bam1_qual(b); - if (g_sol2sanger_tbl[30] == 0) { - for (l = 0; l != 128; ++l) { - g_sol2sanger_tbl[l] = (int)(10.0 * log(1.0 + pow(10.0, (l - 64 + 33) / 10.0)) / log(10.0) + .499); - if (g_sol2sanger_tbl[l] >= 93) g_sol2sanger_tbl[l] = 93; - } - } - for (l = 0; l < b->core.l_qseq; ++l) { - int q = qual[l]; - if (q > 127) q = 127; - qual[l] = g_sol2sanger_tbl[q]; - } -} - -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_rg || g_rghash) { - uint8_t *s = bam_aux_get(b, "RG"); - if (s) { - if (g_rg) return (strcmp(g_rg, (char*)(s + 1)) == 0)? 0 : 1; - if (g_rghash) { - khint_t k = kh_get(rg, g_rghash, (char*)(s + 1)); - return (k != kh_end(g_rghash))? 0 : 1; - } - } - } - if (g_library) { - const char *p = bam_get_library((bam_header_t*)h, b); - return (p && strcmp(p, g_library) == 0)? 0 : 1; - } - 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, slx2sngr = 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, *fn_rg = 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:CR:")) >= 0) { - switch (c) { - case 'C': slx2sngr = 1; break; - 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 'R': fn_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); // potential memory leak... - - // read the list of read groups - if (fn_rg) { - FILE *fp_rg; - char buf[1024]; - int ret; - g_rghash = kh_init(rg); - fp_rg = fopen(fn_rg, "r"); - while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but bear me... - kh_put(rg, g_rghash, strdup(buf), &ret); // we'd better check duplicates... - fclose(fp_rg); - } - - // 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)) { - if (slx2sngr) sol2sanger(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); free(fn_rg); - if (g_rghash) { - khint_t k; - for (k = 0; k < kh_end(g_rghash); ++k) - if (kh_exist(g_rghash, k)) free((char*)kh_key(g_rghash, k)); - kh_destroy(rg, g_rghash); - } - samclose(in); - samclose(out); - return ret; -} - -static int usage(int is_long_help) -{ - fprintf(stderr, "\n"); - fprintf(stderr, "Usage: samtools view [options] | [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, " -R FILE list of read groups to be outputted [null]\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 \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; -}