rc_t CGWriterEvdInt_Make(const CGWriterEvdInt** cself, TEvidenceIntervalsData** data,
VDatabase* db, const ReferenceMgr* rmgr, const uint32_t options)
{
rc_t rc = 0;
CGWriterEvdInt* self;
if( cself == NULL || db == NULL ) {
return RC(rcExe, rcFormatter, rcConstructing, rcParam, rcNull);
}
self = calloc(1, sizeof(*self));
if( self == NULL ) {
rc = RC(rcExe, rcFormatter, rcConstructing, rcMemory, rcExhausted);
} else {
if( (rc = TableWriterAlgn_Make(&self->writer, db, ewalgn_tabletype_EvidenceInterval, 0)) == 0 ) {
self->algn.read_start.buffer = &self->match.read_start;
self->algn.read_len.buffer = &self->match.read_len;
self->algn.has_ref_offset.buffer = self->match.has_ref_offset;
self->algn.ref_offset.buffer = self->match.ref_offset;
self->algn.has_mismatch.buffer = self->match.has_mismatch;
self->algn.mismatch.buffer = self->match.mismatch;
self->algn.ref_id.buffer = &self->match.ref_id;
self->algn.ref_id.elements = 1;
self->algn.ref_start.buffer = &self->match.ref_start;
self->algn.ref_start.elements = 1;
self->match.ref_orientation = false;
self->algn.ref_orientation.buffer = &self->match.ref_orientation;
self->algn.ref_orientation.elements = 1;
self->algn.mapq.buffer = &self->match.mapq;
self->algn.mapq.elements = 1;
self->algn.alingment_ids.buffer = self->dnbs_ids;
self->rmgr = rmgr;
*data = &self->data;
}
}
if( rc == 0 ) {
*cself = self;
} else {
CGWriterEvdInt_Whack(self, false, NULL);
}
return rc;
}
rc_t CGWriterAlgn_Make(const CGWriterAlgn** cself, TMappingsData** data, VDatabase* db, const ReferenceMgr* rmgr,
uint32_t min_mapq, bool single_mate, uint32_t cluster_size)
{
rc_t rc = 0;
CGWriterAlgn* self;
if( cself == NULL || db == NULL ) {
return RC(rcExe, rcFormatter, rcConstructing, rcParam, rcNull);
}
self = calloc(1, sizeof(*self));
if( self == NULL ) {
rc = RC(rcExe, rcFormatter, rcConstructing, rcMemory, rcExhausted);
} else {
if( (rc = TableWriterAlgn_Make(&self->primary, db,
ewalgn_tabletype_PrimaryAlignment, ewalgn_co_SEQ_SPOT_ID | ewalgn_co_unsorted)) != 0 ){
LOGERR(klogErr, rc, "primary alignment table");
} else if( (rc = TableWriterAlgn_Make(&self->secondary, db,
ewalgn_tabletype_SecondaryAlignment, ewalgn_co_SEQ_SPOT_ID | ewalgn_co_unsorted)) != 0 ) {
LOGERR(klogErr, rc, "secondary alignment table");
} else {
int i;
/* interconnect buffers */
for(i = 0; i < CG_MAPPINGS_MAX; i++) {
self->algn[i].seq_spot_id.buffer = &self->match[i].seq_spot_id;
self->algn[i].seq_spot_id.elements = 1;
self->algn[i].seq_read_id.buffer = &self->match[i].seq_read_id;
self->algn[i].seq_read_id.elements = 1;
self->algn[i].read_start.buffer = &self->match[i].read_start;
self->algn[i].read_len.buffer = &self->match[i].read_len;
self->algn[i].has_ref_offset.buffer = self->match[i].has_ref_offset;
self->algn[i].ref_offset.buffer = self->match[i].ref_offset;
self->algn[i].ref_offset_type.buffer = self->match[i].ref_offset_type;
self->algn[i].ref_id.buffer = &self->match[i].ref_id;
self->algn[i].ref_start.buffer = &self->match[i].ref_start;
self->algn[i].has_mismatch.buffer = self->match[i].has_mismatch;
self->algn[i].mismatch.buffer = self->match[i].mismatch;
self->algn[i].ref_orientation.buffer = &self->match[i].ref_orientation;
self->algn[i].ref_orientation.elements = 1;
self->algn[i].mapq.buffer = &self->match[i].mapq;
self->algn[i].mapq.elements = 1;
self->algn[i].mate_ref_orientation.buffer = &self->match[i].mate_ref_orientation;
self->algn[i].mate_ref_orientation.elements = 1;
self->algn[i].mate_ref_id.buffer = &self->match[i].mate_ref_id;
self->algn[i].mate_ref_id.elements = 1;
self->algn[i].mate_ref_pos.buffer = &self->match[i].mate_ref_pos;
self->algn[i].mate_ref_pos.elements = 1;
self->algn[i].template_len.buffer = &self->match[i].template_len;
self->algn[i].template_len.elements = 1;
}
self->rmgr = rmgr;
self->min_mapq = min_mapq;
self->single_mate = single_mate;
global_cluster_size = cluster_size;
*data = &self->data;
}
}
if( rc == 0 ) {
*cself = self;
} else {
CGWriterAlgn_Whack(self, false, NULL, NULL);
}
return rc;
}
