void
tmap_sam_io_set_vfo(tmap_sam_io_t *samio, int64_t bam_start_vfo, int64_t bam_end_vfo)
{
samio->bam_end_vfo = bam_end_vfo;
if (bam_start_vfo > 0) {
fprintf(stderr, "seeking to bam virtual file offset %lu\n", bam_start_vfo);
BGZF* bgzf_fp = samio->fp->x.bam;
if (0 > bam_seek(bgzf_fp, bam_start_vfo, SEEK_SET)) {
fprintf(stderr, "error seeking to offset\n");
}
}
}
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);
}
