void SequenceWhack(Sequence *self, bool commit) {
uint64_t dummyRows;
VDatabaseRelease(self->db);
if (self->tbl == NULL)
return;
(void)TableWriterSeq_Whack(self->tbl, commit, &dummyRows);
}
LIB_EXPORT rc_t CC TableWriterSeq_Make(const TableWriterSeq** cself, VDatabase* db,
uint32_t options, char const qual_quantization[])
{
rc_t rc = 0;
TableWriterSeq* self = NULL;
char const *tblName = (options & ewseq_co_ColorSpace) ? "CS_SEQUENCE" : "SEQUENCE";
options |= ewseq_co_SaveQual; /* TODO: remove when ready */
if( cself == NULL || db == NULL ) {
rc = RC(rcAlign, rcFormatter, rcConstructing, rcParam, rcNull);
} else {
self = calloc(1, sizeof(*self));
if( self == NULL ) {
rc = RC(rcAlign, rcFormatter, rcConstructing, rcMemory, rcExhausted);
} else {
memcpy(self->cols, TableWriterSeq_cols, sizeof(TableWriterSeq_cols));
if( options & ewseq_co_AlignData ) {
self->cols[ewseq_cn_TMP_KEY_ID].flags |= ewcol_Ignore;
} else {
self->cols[ewseq_cn_PRIMARY_ALIGNMENT_ID].flags |= ewcol_Ignore;
self->cols[ewseq_cn_ALIGNMENT_COUNT].flags |= ewcol_Ignore;
}
if(options & ewseq_co_NoLabelData) {
self->cols[ewseq_cn_LABEL].flags |= ewcol_Ignore;
self->cols[ewseq_cn_LABEL_LEN].flags |= ewcol_Ignore;
self->cols[ewseq_cn_LABEL_START].flags |= ewcol_Ignore;
}
if(options & ewseq_co_ColorSpace) {
self->cols[ewseq_cn_READ].flags |= ewcol_Ignore;
self->cols[ewseq_cn_CSREAD].flags &= ~ewcol_Ignore;
self->cols[ewseq_cn_CSKEY].flags &= ~ewcol_Ignore;
}
if( options & ewseq_co_SpotGroup) {
self->cols[ewseq_cn_SPOT_GROUP].flags &= ~ewcol_Ignore;
}
if( options & ewseq_co_TI) {
self->cols[ewseq_cn_TI].flags &= ~ewcol_Ignore;
}
if( options & ewseq_co_SpotName) {
self->cols[ewseq_cn_NAME].flags &= ~ewcol_Ignore;
}
if( (rc = TableWriter_Make(&self->base, db, tblName, "SEQUENCE")) == 0 ) {
rc = TableWriter_AddCursor(self->base, self->cols, sizeof(self->cols)/sizeof(self->cols[0]), &self->cursor_id);
}
}
if( rc == 0 ) {
self->options = options;
if (qual_quantization && strcmp(qual_quantization, "0") == 0) {
self->options |= ewseq_co_FullQuality;
}
if( !(self->options & ewseq_co_FullQuality) ) {
char const *quant_string = qual_quantization;
if (quant_string == NULL || strcmp(quant_string, "1") == 0) {
quant_string = "1:10,10:20,20:30,30:-";
} else if (strcmp(quant_string, "2") == 0) {
quant_string = "1:30,30:-";
}
if (!TableWriterSeq_InitQuantMatrix(self->discrete_qual, quant_string)) {
rc = RC(rcAlign, rcFormatter, rcConstructing, rcParam, rcInvalid);
}
}
}
}
if( rc == 0 ) {
*cself = self;
ALIGN_DBG("table %s", "created");
} else {
TableWriterSeq_Whack(self, false, NULL);
ALIGN_DBGERR(rc);
}
return rc;
}
