SEXP bamfile_isopen(SEXP ext)
{
int ans = FALSE;
if (NULL != BAMFILE(ext)) {
_checkext(ext, BAMFILE_TAG, "isOpen");
ans = NULL != BAMFILE(ext)->file;
}
return ScalarLogical(ans);
}
BAM_DATA
_init_BAM_DATA(SEXP ext, SEXP space, SEXP flag, SEXP isSimpleCigar,
SEXP tagFilter, SEXP mapqFilter, int reverseComplement,
int yieldSize, int obeyQname, int asMates,
char qnamePrefixEnd, char qnameSuffixStart, void *extra)
{
int nrange = R_NilValue == space ? 1 : LENGTH(VECTOR_ELT(space, 0));
BAM_DATA bd =
_Calloc_BAM_DATA(1 == nrange ?
5 * BAM_INIT_SIZE : BAM_INIT_SIZE, 32768);
bd->parse_status = BAM_PARSE_STATUS_OK;
bd->bfile = BAMFILE(ext);
bd->irange = bd->bfile->irange0;
bd->nrange = nrange;
bd->irec = bd->iparsed = 0;
bd->keep_flag[0] = INTEGER(flag)[0];
bd->keep_flag[1] = INTEGER(flag)[1];
bd->cigar_flag = LOGICAL(isSimpleCigar)[0];
bd->tagfilter = _tagFilter_as_C_types(tagFilter);
int mapqfilter = INTEGER(mapqFilter)[0];
bd->mapqfilter = mapqfilter == NA_INTEGER ? 0 : mapqfilter; /* uint32_t */
bd->reverseComplement = reverseComplement;
bd->yieldSize = yieldSize;
bd->obeyQname = obeyQname;
bd->asMates = asMates;
bd->qnamePrefixEnd = qnamePrefixEnd;
bd->qnameSuffixStart = qnameSuffixStart;
bd->extra = extra;
return bd;
}
static void _bamfile_finalizer(SEXP ext)
{
if (NULL == R_ExternalPtrAddr(ext))
return;
_bamfile_close(ext);
BAM_FILE bfile = BAMFILE(ext);
Free(bfile);
R_SetExternalPtrAddr(ext, NULL);
}
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);
}
static void _bamfile_close(SEXP ext)
{
BAM_FILE bfile = BAMFILE(ext);
if (NULL != bfile->file)
samclose(bfile->file);
if (NULL != bfile->index)
bam_index_destroy(bfile->index);
if (NULL != bfile->iter)
bam_mate_iter_destroy(bfile->iter);
if (NULL != bfile->pbuffer)
pileup_pbuffer_destroy(bfile->pbuffer);
bfile->file = NULL;
bfile->index = NULL;
bfile->iter = NULL;
}
SEXP _read_bam_header(SEXP ext, SEXP what)
{
samfile_t *sfile = BAMFILE(ext)->file;
bam_header_t *header = sfile->header;
SEXP ans = PROTECT(NEW_LIST(2));
SEXP nms = NEW_CHARACTER(2);
setAttrib(ans, R_NamesSymbol, nms);
SET_STRING_ELT(nms, 0, mkChar("targets"));
SET_STRING_ELT(nms, 1, mkChar("text"));
if (LOGICAL(what)[0] == TRUE) { /* 'targets' */
int n_elts = header->n_targets;
SET_VECTOR_ELT(ans, 0, NEW_INTEGER(n_elts));
SEXP tlen = VECTOR_ELT(ans, 0); /* target length */
SEXP tnm = NEW_CHARACTER(n_elts); /* target name */
setAttrib(tlen, R_NamesSymbol, tnm);
for (int j = 0; j < n_elts; ++j) {
INTEGER(tlen)[j] = header->target_len[j];
SET_STRING_ELT(tnm, j, mkChar(header->target_name[j]));
}
}
if (LOGICAL(what)[1] == TRUE) { /* 'text' */
int n_text_elts = 0;
for (int i = 0; i < header->l_text; ++i)
if (header->text[i] == '\n')
n_text_elts += 1;
SET_VECTOR_ELT(ans, 1, NEW_LIST(n_text_elts));
SEXP text = VECTOR_ELT(ans, 1);
SEXP tag = NEW_CHARACTER(n_text_elts);
setAttrib(text, R_NamesSymbol, tag);
int start = 0, end;
for (int i = 0; i < n_text_elts; ++i) {
int n_elts = header->text[start] == '\n' ? 0 : 1;
end = start;
while (header->text[end] != '\n') {
if (header->text[end] == '\t')
++n_elts;
++end;
}
if (n_elts == 0) {
SET_VECTOR_ELT(text, i, NEW_CHARACTER(0));
/* SET_STRING_ELT(tag, i, mkChar("")); */
start = end + 1;
continue;
}
SET_VECTOR_ELT(text, i, NEW_CHARACTER(n_elts - 1));
SEXP elts = VECTOR_ELT(text, i);
for (int j = 0; j < n_elts; ++j) {
end = start;
while (header->text[end] != '\t' && header->text[end] != '\n')
++end;
SEXP elt = mkCharLen(&header->text[start], end - start);
if (j == 0) /* tag */
SET_STRING_ELT(tag, i, elt);
else
SET_STRING_ELT(elts, j - 1, elt);
start = end + 1;
}
}
}
UNPROTECT(1);
return ans;
}