static BAM_FILE _bamfile_open_r(SEXP filename, SEXP indexname, SEXP filemode)
{
BAM_FILE bfile = (BAM_FILE) Calloc(1, _BAM_FILE);
bfile->file = NULL;
if (0 != Rf_length(filename)) {
const char *cfile = translateChar(STRING_ELT(filename, 0));
bfile->file = _bam_tryopen(cfile, CHAR(STRING_ELT(filemode, 0)), 0);
if ((bfile->file->type & TYPE_BAM) != 1) {
samclose(bfile->file);
Free(bfile);
Rf_error("'filename' is not a BAM file\n file: %s", cfile);
}
bfile->pos0 = bam_tell(bfile->file->x.bam);
bfile->irange0 = 0;
}
bfile->index = NULL;
if (0 != Rf_length(indexname)) {
const char *cindex = translateChar(STRING_ELT(indexname, 0));
bfile->index = _bam_tryindexload(cindex);
if (NULL == bfile->index) {
samclose(bfile->file);
Free(bfile);
Rf_error("failed to open BAM index\n index: %s\n", cindex);
}
}
bfile->iter = NULL;
bfile->pbuffer = NULL;
return bfile;
}
SEXP bamfile_isincomplete(SEXP ext)
{
int ans = FALSE;
BAM_FILE bfile;
if (NULL != BAMFILE(ext)) {
_checkext(ext, BAMFILE_TAG, "isIncomplete");
bfile = BAMFILE(ext);
if (NULL != bfile && NULL != bfile->file) {
/* heuristic: can we read a record? bam_seek does not
* support SEEK_END */
off_t offset = bam_tell(bfile->file->x.bam);
char buf;
ans = bam_read(bfile->file->x.bam, &buf, 1) > 0;
bam_seek(bfile->file->x.bam, offset, SEEK_SET);
}
}
return ScalarLogical(ans);
}
int32_t
tmap_sam_io_read(tmap_sam_io_t *samio, tmap_sam_t *sam)
{
if(NULL != sam->b) {
bam_destroy1(sam->b);
}
sam->b = bam_init1();
// check if we're past optional end bam virtual file offset
if (samio->bam_end_vfo > 0) {
BGZF* bgzf_fp = samio->fp->x.bam;
if (bam_tell(bgzf_fp) >= samio->bam_end_vfo) {
fprintf(stderr, "stopping at bam virtual file offset %lu\n", samio->bam_end_vfo);
return -1;
}
}
if(0 < samread(samio->fp, sam->b)) {
char *str;
int32_t i, len;
// name
str = bam1_qname(sam->b);
len = strlen(str);
tmap_sam_io_update_string(&sam->name, str, len);
sam->name->s[len] = '\0';
// seq and qual
len = sam->b->core.l_qseq;
tmap_sam_io_update_string(&sam->seq, NULL, len);
tmap_sam_io_update_string(&sam->qual, (char*)bam1_qual(sam->b), len);
for(i=0;i<len;i++) {
sam->seq->s[i] = bam_nt16_rev_table[bam1_seqi(bam1_seq(sam->b), i)];
sam->qual->s[i] = QUAL2CHAR(sam->qual->s[i]);
}
sam->seq->s[len] = sam->qual->s[len] = '\0';
// reverse compliment if necessary
if((sam->b->core.flag & BAM_FREVERSE)) {
tmap_sam_reverse_compliment(sam);
}
return 1;
}
return -1;
}
static BAM_FILE _bamfile_open_w(SEXP file0, SEXP file1)
{
samfile_t *infile, *outfile;
BAM_FILE bfile;
if (0 == Rf_length(file1))
Rf_error("'file1' must be a character(1) path to a valid bam file");
infile = _bam_tryopen(translateChar(STRING_ELT(file1, 0)), "rb", 0);
outfile = _bam_tryopen(translateChar(STRING_ELT(file0, 0)), "wb",
infile->header);
samclose(infile);
bfile = (BAM_FILE) Calloc(1, _BAM_FILE);
bfile->file = outfile;
bfile->pos0 = bam_tell(bfile->file->x.bam);
bfile->irange0 = 0;
return bfile;
}
