samfile_t* samopen_in(quip_reader_t reader, void* reader_data, bool binary, void* aux)
{
samfile_t *fp;
fp = (samfile_t*)calloc(1, sizeof(samfile_t));
fp->type |= TYPE_READ;
if (binary) { // binary
fp->type |= TYPE_BAM;
fp->x.bam = bam_open_in(reader, reader_data);
if (fp->x.bam == 0) goto open_err_ret;
fp->header = bam_header_read(fp->x.bam);
} else { // text
fp->x.tamr = sam_open_in(reader, reader_data);
if (fp->x.tamr == 0) goto open_err_ret;
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_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 && 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);
}
return fp;
open_err_ret:
free(fp);
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 (strchr(mode, 'r')) { // read
fp->type |= TYPE_READ;
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;
fp->header = bam_header_read(fp->x.bam);
} else { // text
fp->x.tamr = sam_open(fn);
if (fp->x.tamr == 0) goto open_err_ret;
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_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 && 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 (strchr(mode, 'w')) { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
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, 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.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 (strchr(mode, 'h')) {
int i;
bam_header_t *alt;
// parse the header text
alt = bam_header_init();
alt->l_text = fp->header->l_text; alt->text = fp->header->text;
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); // 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 && 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]);
}
bam_header_destroy(alt);
}
}
}
return fp;
open_err_ret:
free(fp);
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
fp->type |= TYPE_READ;
if (mode[1] == '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;
fp->header = bam_header_read(fp->x.bam);
} else { // text
fp->x.tamr = sam_open(fn);
if (fp->x.tamr == 0) goto open_err_ret;
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);
fp->header = sam_header_read2((const char*)aux);
}
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);
}
} else if (mode[0] == 'w') { // write
fp->header = bam_header_dup((const bam_header_t*)aux);
if (mode[1] == 'b') { // binary
fp->type |= TYPE_BAM;
fp->x.bam = strcmp(fn, "-")? bam_open(fn, "w") : bam_dopen(fileno(stdout), "w");
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;
// write header
if (strstr(mode, "h")) {
int i;
bam_header_t *alt;
// parse the header text
alt = bam_header_init();
alt->l_text = fp->header->l_text; alt->text = fp->header->text;
sam_header_parse(alt);
alt->l_text = 0; alt->text = 0;
// check if there are @SQ lines in the header
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");
fwrite(fp->header->text, 1, fp->header->l_text, fp->x.tamw);
} 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]);
}
bam_header_destroy(alt);
}
}
}
return fp;
open_err_ret:
free(fp);
return 0;
}
