LIB_EXPORT rc_t CC AlignAccessDBEnumerateAlignments(const AlignAccessDB *self, AlignAccessAlignmentEnumerator **align_enum) {
rc_t rc;
*align_enum = NULL;
rc = BAMFileRewind(self->innerSelf);
if (rc)
return rc;
rc = AlignAccessDBMakeEnumerator(self, align_enum);
if (rc)
return rc;
return AlignAccessAlignmentEnumeratorNext(*align_enum);
}
LIB_EXPORT
rc_t CC AlignAccessDBWindowedAlignments(const AlignAccessDB *self,
AlignAccessAlignmentEnumerator **align_enum,
const char *refSeqName, uint64_t pos, uint64_t wsize
)
{
AlignAccessAlignmentEnumerator *lhs;
unsigned i, n;
const BAMRefSeq *rs;
uint64_t endpos = pos + wsize;
rc_t rc;
BAMFileSlice *slice;
*align_enum = NULL;
BAMFileGetRefSeqCount(self->innerSelf, &n);
for (i = 0; i != n; ++i) {
BAMFileGetRefSeq(self->innerSelf, i, &rs);
if (strcmp(refSeqName, rs->name) == 0)
break;
}
if (i == n || pos >= rs->length) {
return RC(rcAlign, rcTable, rcConstructing, rcParam, rcInvalid);
}
if (endpos > rs->length || wsize == 0)
endpos = rs->length;
rc = BAMFileMakeSlice(self->innerSelf, &slice, i, pos, endpos);
if (rc == 0 && slice == NULL)
return RC(rcAlign, rcTable, rcConstructing, rcMemory, rcExhausted);
if ( rc != 0 )
{
if ( GetRCState( rc ) == rcNotFound && GetRCObject( rc ) == (enum RCObject)rcData )
rc = AlignAccessAlignmentEnumeratorEOFCode;
return rc;
}
rc = AlignAccessDBMakeEnumerator(self, &lhs);
if (rc)
return rc;
lhs->refSeqID = i;
lhs->endpos = endpos;
lhs->startpos = pos;
lhs->slice = slice;
*align_enum = lhs;
return AlignAccessAlignmentEnumeratorNext(*align_enum);
}
void run()
{
GUARD();
AlignAccessAlignmentEnumerator* iter = 0;
rc_t rc;
{
GUARD();
rc = AlignAccessDBWindowedAlignments(bam, &iter, ref, 0, 0);
}
while ( rc == 0 ) {
++count;
GUARD();
rc = AlignAccessAlignmentEnumeratorNext(iter);
}
if ( !AlignAccessAlignmentEnumeratorIsEOF(rc) ) {
CALL(rc);
}
{
GUARD();
AlignAccessAlignmentEnumeratorRelease(iter);
}
}
