LIB_EXPORT rc_t CC AlignAccessAlignmentEnumeratorNext(const AlignAccessAlignmentEnumerator *cself) {
rc_t rc;
AlignAccessAlignmentEnumerator *self = (AlignAccessAlignmentEnumerator *)cself;
int32_t refSeqID;
AGAIN:
if (self->innerSelf != NULL) {
BAMAlignmentRelease(self->innerSelf);
self->innerSelf = NULL;
}
if (self->atend != 0)
return AlignAccessAlignmentEnumeratorEOFCode;
if (self->slice == NULL) {
rc = BAMFileRead2(self->parent->innerSelf, &self->innerSelf);
if (rc) {
if (GetRCState(rc) == rcNotFound && GetRCObject(rc) == rcRow) {
self->atend = 1;
rc = AlignAccessAlignmentEnumeratorEOFCode;
}
}
return rc;
}
rc = BAMFileReadSlice(self->parent->innerSelf, &self->innerSelf, self->slice);
if (rc) {
if (GetRCState(rc) == rcNotFound && GetRCObject(rc) == rcRow) {
self->atend = 1;
rc = AlignAccessAlignmentEnumeratorEOFCode;
}
return rc;
}
if (!BAMAlignmentIsMapped(self->innerSelf))
goto AGAIN;
BAMAlignmentGetRefSeqId(self->innerSelf, &refSeqID);
if (self->refSeqID != refSeqID) {
self->atend = 1;
rc = AlignAccessAlignmentEnumeratorEOFCode;
}
else if (self->endpos != 0) {
int64_t pos;
uint32_t length;
BAMAlignmentGetPosition2(self->innerSelf, &pos, &length);
if (pos >= (int64_t)self->endpos) {
self->atend = 1;
rc = AlignAccessAlignmentEnumeratorEOFCode;
}
else {
int64_t const endpos = pos + length;
if (endpos <= self->startpos)
goto AGAIN;
}
}
return rc;
}
LIB_EXPORT rc_t CC AlignAccessAlignmentEnumeratorGetRefSeqLen(
const AlignAccessAlignmentEnumerator *self,
uint32_t *reflen
)
{
rc_t rc;
uint32_t length;
int64_t pos;
rc = BAMAlignmentGetPosition2(self->innerSelf, &pos, &length);
if (rc)
return rc;
if (pos < 0)
return RC(rcAlign, rcTable, rcAccessing, rcData, rcNotFound);
*reflen = length;
return 0;
}
