X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=pysam.git;a=blobdiff_plain;f=samtools%2Fsam_view.c.pysam.c;fp=samtools%2Fsam_view.c.pysam.c;h=2c4736336ee2e27150ce47d15d661e190c580888;hp=0000000000000000000000000000000000000000;hb=bd0c3067c187d1f718004fb38acc093af8810a02;hpb=1b740fc70684c92a5e2293013217d5a2fd661d8a diff --git a/samtools/sam_view.c.pysam.c b/samtools/sam_view.c.pysam.c new file mode 100644 index 0000000..2c47363 --- /dev/null +++ b/samtools/sam_view.c.pysam.c @@ -0,0 +1,353 @@ +#include "pysam.h" + +#include +#include +#include +#include +#include +#include "sam_header.h" +#include "sam.h" +#include "faidx.h" +#include "kstring.h" +#include "khash.h" +KHASH_SET_INIT_STR(rg) + +// When counting records instead of printing them, +// data passed to the bam_fetch callback is encapsulated in this struct. +typedef struct { + bam_header_t *header; + int *count; +} count_func_data_t; + +typedef khash_t(rg) *rghash_t; + +static 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 *g_bed; + +void *bed_read(const char *fn); +void bed_destroy(void *_h); +int bed_overlap(const void *_h, const char *chr, int beg, int end); + +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_bed && b->core.tid >= 0 && !bed_overlap(g_bed, h->target_name[b->core.tid], b->core.pos, bam_calend(&b->core, bam1_cigar(b)))) + 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; +} + +static char *drop_rg(char *hdtxt, rghash_t h, int *len) +{ + char *p = hdtxt, *q, *r, *s; + kstring_t str; + memset(&str, 0, sizeof(kstring_t)); + while (1) { + int toprint = 0; + q = strchr(p, '\n'); + if (q == 0) q = p + strlen(p); + if (q - p < 3) break; // the line is too short; then stop + if (strncmp(p, "@RG\t", 4) == 0) { + int c; + khint_t k; + if ((r = strstr(p, "\tID:")) != 0) { + r += 4; + for (s = r; *s != '\0' && *s != '\n' && *s != '\t'; ++s); + c = *s; *s = '\0'; + k = kh_get(rg, h, r); + *s = c; + if (k != kh_end(h)) toprint = 1; + } + } else toprint = 1; + if (toprint) { + kputsn(p, q - p, &str); kputc('\n', &str); + } + p = q + 1; + } + *len = str.l; + return str.s; +} + +// callback function for bam_fetch() that prints nonskipped records +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; +} + +// callback function for bam_fetch() that counts nonskipped records +static int count_func(const bam1_t *b, void *data) +{ + if (!__g_skip_aln(((count_func_data_t*)data)->header, b)) { + (*((count_func_data_t*)data)->count)++; + } + 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, compress_level = -1, is_bamout = 0, slx2sngr = 0, is_count = 0; + int of_type = BAM_OFDEC, is_long_help = 0; + int count = 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, "Sbct:h1Ho:q:f:F:ul:r:xX?T:CR:L:")) >= 0) { + switch (c) { + case 'c': is_count = 1; break; + 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': compress_level = 0; break; + case '1': compress_level = 1; break; + case 'l': g_library = strdup(optarg); break; + case 'L': g_bed = bed_read(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 (compress_level >= 0) 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 (compress_level >= 0) { + char tmp[2]; + tmp[0] = compress_level + '0'; tmp[1] = '\0'; + strcat(out_mode, tmp); + } + 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(pysamerr, "[main_samview] fail to open \"%s\" for reading.\n", argv[optind]); + ret = 1; + goto view_end; + } + if (in->header == 0) { + fprintf(pysamerr, "[main_samview] fail to read the header from \"%s\".\n", argv[optind]); + ret = 1; + goto view_end; + } + if (g_rghash) { // FIXME: I do not know what "bam_header_t::n_text" is for... + char *tmp; + int l; + tmp = drop_rg(in->header->text, g_rghash, &l); + free(in->header->text); + in->header->text = tmp; + in->header->l_text = l; + } + if (!is_count && (out = samopen(fn_out? fn_out : "-", out_mode, in->header)) == 0) { + fprintf(pysamerr, "[main_samview] fail to open \"%s\" for writing.\n", fn_out? fn_out : "standard output"); + ret = 1; + 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); + if (!is_count) samwrite(out, b); // write the alignment to `out' + count++; + } + } + if (r < -1) { + fprintf(pysamerr, "[main_samview] truncated file.\n"); + ret = 1; + } + 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(pysamerr, "[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, result; + 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(pysamerr, "[main_samview] region \"%s\" specifies an unknown reference name. Continue anyway.\n", argv[i]); + continue; + } + // fetch alignments + if (is_count) { + count_func_data_t count_data = { in->header, &count }; + result = bam_fetch(in->x.bam, idx, tid, beg, end, &count_data, count_func); + } else + result = bam_fetch(in->x.bam, idx, tid, beg, end, out, view_func); + if (result < 0) { + fprintf(pysamerr, "[main_samview] retrieval of region \"%s\" failed due to truncated file or corrupt BAM index file\n", argv[i]); + ret = 1; + break; + } + } + bam_index_destroy(idx); // destroy the BAM index + } + +view_end: + if (is_count && ret == 0) { + printf("%d\n", count); + } + // 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_bed) bed_destroy(g_bed); + 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); + if (!is_count) + samclose(out); + return ret; +} + +static int usage(int is_long_help) +{ + fprintf(pysamerr, "\n"); + fprintf(pysamerr, "Usage: samtools view [options] | [region1 [...]]\n\n"); + fprintf(pysamerr, "Options: -b output BAM\n"); + fprintf(pysamerr, " -h print header for the SAM output\n"); + fprintf(pysamerr, " -H print header only (no alignments)\n"); + fprintf(pysamerr, " -S input is SAM\n"); + fprintf(pysamerr, " -u uncompressed BAM output (force -b)\n"); + fprintf(pysamerr, " -1 fast compression (force -b)\n"); + fprintf(pysamerr, " -x output FLAG in HEX (samtools-C specific)\n"); + fprintf(pysamerr, " -X output FLAG in string (samtools-C specific)\n"); + fprintf(pysamerr, " -c print only the count of matching records\n"); + fprintf(pysamerr, " -L FILE output alignments overlapping the input BED FILE [null]\n"); + fprintf(pysamerr, " -t FILE list of reference names and lengths (force -S) [null]\n"); + fprintf(pysamerr, " -T FILE reference sequence file (force -S) [null]\n"); + fprintf(pysamerr, " -o FILE output file name [stdout]\n"); + fprintf(pysamerr, " -R FILE list of read groups to be outputted [null]\n"); + fprintf(pysamerr, " -f INT required flag, 0 for unset [0]\n"); + fprintf(pysamerr, " -F INT filtering flag, 0 for unset [0]\n"); + fprintf(pysamerr, " -q INT minimum mapping quality [0]\n"); + fprintf(pysamerr, " -l STR only output reads in library STR [null]\n"); + fprintf(pysamerr, " -r STR only output reads in read group STR [null]\n"); + fprintf(pysamerr, " -? longer help\n"); + fprintf(pysamerr, "\n"); + if (is_long_help) + fprintf(pysamerr, "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(pysamerr, "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; +}