static
rc_t DB_Fini(const SParam* p, DB_Handle* h, bool drop)
{
rc_t rc = 0, rc2;
/* THIS FUNCTION MAKES NO ATTEMPT TO PRESERVE INITIAL ERROR CODES
EACH SUCCESSIVE ERROR OVERWRITES THE PREVIOUS CODE */
if( h != NULL ) {
PLOGMSG(klogInfo, (klogInfo, "Fini SEQUENCE", "severity=status"));
if( (rc2 = CGWriterSeq_Whack(h->wseq, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wseq = NULL;
h->reads = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini (PRI&SEC)_ALIGNMENT", "severity=status"));
if( (rc2 = CGWriterAlgn_Whack(h->walgn, !drop, NULL, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->walgn = NULL;
h->mappings = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini EVIDENCE_INTERVAL", "severity=status"));
if( (rc2 = CGWriterEvdInt_Whack(h->wev_int, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wev_int = NULL;
h->ev_int = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini EVIDENCE_ALIGNMENT", "severity=status"));
if( (rc2 = CGWriterEvdDnbs_Whack(h->wev_dnb, !drop, NULL)) != 0 && !drop ) {
drop = true;
rc = rc2;
}
h->wev_dnb = NULL;
h->ev_dnb = NULL;
PLOGMSG(klogInfo, (klogInfo, "Fini calculating reference coverage", "severity=status"));
if( (rc2 = ReferenceMgr_Release(h->rmgr, !drop, NULL, drop ? false : true)) != 0 && !drop ) {
drop = true;
rc = rc2;
LOGERR(klogErr, rc, "Failed calculating reference coverage");
}
h->rmgr = NULL;
if( rc == 0 )
{
KMetadata* meta;
if( (rc = VDatabaseOpenMetadataUpdate(h->db, &meta)) == 0 ) {
KMDataNode *node;
if( (rc = KMetadataOpenNodeUpdate(meta, &node, "/")) == 0 ) {
if( (rc = KLoaderMeta_Write(node, p->argv0, __DATE__, "Complete Genomics", KAppVersion())) != 0 ) {
LOGERR(klogErr, rc, "Cannot update loader meta");
}
KMDataNodeRelease(node);
}
KMetadataRelease(meta);
}
}
PLOGMSG(klogInfo, (klogInfo, "Fini VDatabaseRelease", "severity=status"));
VDatabaseRelease(h->db);
h->db = NULL;
VSchemaRelease(h->schema);
h->schema = NULL;
if( drop || rc != 0 ) {
rc2 = VDBManagerDrop(h->mgr, kptDatabase, p->out);
if( GetRCState(rc2) == rcNotFound ) {
/* WHAT WOULD BE THE POINT OF RESETTING "rc" TO ZERO? */
rc = 0;
} else if( rc2 != 0 ) {
if ( rc == 0 )
rc = rc2;
PLOGERR(klogErr, (klogErr, rc2, "cannot drop db at '$(path)'", PLOG_S(path), p->out));
}
}
VDBManagerRelease(h->mgr);
h->mgr = 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;
}
