X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sam.c;h=fa11df6c12b1abc589415d4d11fe269067ecd765;hb=0ccd9d36ebf35ce620a8248ecf4336c84065e6c0;hp=8411d81f0af8b19e04cc1ffc77e1f741efd6987b;hpb=94bf0806a9697592e897f65c0fe8e460451d2021;p=samtools.git diff --git a/sam.c b/sam.c index 8411d81..fa11df6 100644 --- a/sam.c +++ b/sam.c @@ -1,4 +1,6 @@ #include +#include +#include "faidx.h" #include "sam.h" #define TYPE_BAM 1 @@ -10,7 +12,7 @@ bam_header_t *bam_header_dup(const bam_header_t *h0) int i; h = bam_header_init(); *h = *h0; - h->hash = 0; + h->hash = h->dict = h->rg2lib = 0; h->text = (char*)calloc(h->l_text + 1, 1); memcpy(h->text, h0->text, h->l_text); h->target_len = (uint32_t*)calloc(h->n_targets, 4); @@ -21,14 +23,33 @@ bam_header_t *bam_header_dup(const bam_header_t *h0) } return h; } +static void append_header_text(bam_header_t *header, char* text, int len) +{ + int x = header->l_text + 1; + int y = header->l_text + len + 1; // 1 byte null + if (text == 0) return; + kroundup32(x); + kroundup32(y); + if (x < y) header->text = (char*)realloc(header->text, y); + strncpy(header->text + header->l_text, text, len); // we cannot use strcpy() here. + header->l_text += len; + header->text[header->l_text] = 0; +} + +int samthreads(samfile_t *fp, int n_threads, int n_sub_blks) +{ + if (!(fp->type&1) || (fp->type&2)) return -1; + bgzf_mt(fp->x.bam, n_threads, n_sub_blks); + return 0; +} samfile_t *samopen(const char *fn, const char *mode, const void *aux) { samfile_t *fp; fp = (samfile_t*)calloc(1, sizeof(samfile_t)); - if (mode[0] == 'r') { // read + if (strchr(mode, 'r')) { // read fp->type |= TYPE_READ; - if (mode[1] == 'b') { // binary + if (strchr(mode, 'b')) { // binary fp->type |= TYPE_BAM; fp->x.bam = strcmp(fn, "-")? bam_open(fn, "r") : bam_dopen(fileno(stdin), "r"); if (fp->x.bam == 0) goto open_err_ret; @@ -39,26 +60,38 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux) fp->header = sam_header_read(fp->x.tamr); if (fp->header->n_targets == 0) { // no @SQ fields if (aux) { // check if aux is present - bam_header_destroy(fp->header); + bam_header_t *textheader = fp->header; fp->header = sam_header_read2((const char*)aux); + if (fp->header == 0) goto open_err_ret; + append_header_text(fp->header, textheader->text, textheader->l_text); + bam_header_destroy(textheader); } - if (fp->header->n_targets == 0) - fprintf(stderr, "[samopen] empty header.\n"); - } else fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets); + if (fp->header->n_targets == 0 && bam_verbose >= 1) + fprintf(stderr, "[samopen] no @SQ lines in the header.\n"); + } else if (bam_verbose >= 2) fprintf(stderr, "[samopen] SAM header is present: %d sequences.\n", fp->header->n_targets); } - } else if (mode[0] == 'w') { // write + } else if (strchr(mode, 'w')) { // write fp->header = bam_header_dup((const bam_header_t*)aux); - if (mode[1] == 'b') { // binary + if (strchr(mode, 'b')) { // binary + char bmode[3]; + int i, compress_level = -1; + for (i = 0; mode[i]; ++i) if (mode[i] >= '0' && mode[i] <= '9') break; + if (mode[i]) compress_level = mode[i] - '0'; + if (strchr(mode, 'u')) compress_level = 0; + bmode[0] = 'w'; bmode[1] = compress_level < 0? 0 : compress_level + '0'; bmode[2] = 0; fp->type |= TYPE_BAM; - fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w"); + fp->x.bam = strcmp(fn, "-")? bam_open(fn, bmode) : bam_dopen(fileno(stdout), bmode); if (fp->x.bam == 0) goto open_err_ret; bam_header_write(fp->x.bam, fp->header); } else { // text // open file fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout; - if (fp->x.tamr == 0) goto open_err_ret; + if (fp->x.tamw == 0) goto open_err_ret; + if (strchr(mode, 'X')) fp->type |= BAM_OFSTR<<2; + else if (strchr(mode, 'x')) fp->type |= BAM_OFHEX<<2; + else fp->type |= BAM_OFDEC<<2; // write header - if (strstr(mode, "h")) { + if (strchr(mode, 'h')) { int i; bam_header_t *alt; // parse the header text @@ -67,10 +100,10 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux) sam_header_parse(alt); alt->l_text = 0; alt->text = 0; // check if there are @SQ lines in the header - fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); + fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw); // FIXME: better to skip the trailing NULL if (alt->n_targets) { // then write the header text without dumping ->target_{name,len} - if (alt->n_targets != fp->header->n_targets) - fprintf(stderr, "[samopen] inconsistent number of target sequences.\n"); + if (alt->n_targets != fp->header->n_targets && bam_verbose >= 1) + fprintf(stderr, "[samopen] inconsistent number of target sequences. Output the text header.\n"); } else { // then dump ->target_{name,len} for (i = 0; i < fp->header->n_targets; ++i) fprintf(fp->x.tamw, "@SQ\tSN:%s\tLN:%d\n", fp->header->target_name[i], fp->header->target_len[i]); @@ -108,7 +141,7 @@ int samwrite(samfile_t *fp, const bam1_t *b) if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b); else { - char *s = bam_format1(fp->header, b); + char *s = bam_format1_core(fp->header, b, fp->type>>2&3); int l = strlen(s); fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw); free(s); @@ -131,3 +164,23 @@ int sampileup(samfile_t *fp, int mask, bam_pileup_f func, void *func_data) bam_destroy1(b); return 0; } + +char *samfaipath(const char *fn_ref) +{ + char *fn_list = 0; + if (fn_ref == 0) return 0; + fn_list = calloc(strlen(fn_ref) + 5, 1); + strcat(strcpy(fn_list, fn_ref), ".fai"); + if (access(fn_list, R_OK) == -1) { // fn_list is unreadable + if (access(fn_ref, R_OK) == -1) { + fprintf(stderr, "[samfaipath] fail to read file %s.\n", fn_ref); + } else { + if (bam_verbose >= 3) fprintf(stderr, "[samfaipath] build FASTA index...\n"); + if (fai_build(fn_ref) == -1) { + fprintf(stderr, "[samfaipath] fail to build FASTA index.\n"); + free(fn_list); fn_list = 0; + } + } + } + return fn_list; +}