void CVDBCursor::SetParam(const char* name, const CTempString& value) const
{
if ( rc_t rc = VCursorParamsSet
((struct VCursorParams *)GetPointer(),
name, "%.*s", value.size(), value.data()) ) {
NCBI_THROW2_FMT(CSraException, eNotFound,
"Cannot set VDB cursor param: "<<*this<<": "<<name,
rc);
}
}
/* GetSpotId
* convert spot name to spot id
*
* "id" [ OUT ] - return parameter for min(spot_id)-max(spot_id)
*
* "spot_name" [ IN ] - external spot name string
* in platform canonical format.
*/
LIB_EXPORT rc_t CC SRATableGetSpotId ( const SRATable *self,
spotid_t *rslt, const char *spot_name )
{
rc_t rc;
if( self == NULL || spot_name == NULL){
rc=RC(rcSRA, rcTable, rcListing, rcSelf, rcName);
} else {
rc=VCursorParamsSet((struct VCursorParams*)self->curs,"QUERY_BY_NAME" ,spot_name);
if( rc == 0) {
struct {
uint64_t start_id;
uint64_t id_count;
int64_t x;
int64_t y;
} out;
uint32_t idx,len;
rc = VCursorAddColumn(self->curs, &idx, "SPOT_IDS_FOUND");
if( rc == 0 || GetRCState(rc) == rcExists){
rc = VCursorReadDirect(self->curs,1,idx,sizeof(out) * 8,&out, 1 , &len);
if ( rc == 0 ) {
if(out.id_count==1) {
if(rslt) *rslt=out.start_id;
return 0;
} else if(out.id_count > 1) { /*** doing table range scan in Name space - not relying on X and Y***/
uint32_t x_idx;
rc = VCursorAddColumn(self->curs, &x_idx, "X");
if( rc == 0 || GetRCState(rc) == rcExists){
uint32_t y_idx;
rc = VCursorAddColumn(self->curs, &y_idx, "Y");
if(rc == 0 || GetRCState(rc) == rcExists){
spotid_t rowid;
for(rowid = out.start_id; rowid < out.start_id + out.id_count; rowid ++){
int32_t x,y;
rc = VCursorReadDirect(self->curs,rowid,x_idx,32,&x,1, &len);
if(rc == 0){
rc = VCursorReadDirect(self->curs,rowid,y_idx,32,&y,1, &len);
if(rc == 0 && x==out.x && y==out.y){
if(rslt) *rslt=rowid;
return 0;
}
}
}
}
}
}
rc = RC ( rcSRA, rcIndex, rcSearching, rcColumn, rcNotFound );
}
}
}
}
return rc;
}
rc_t runChecks(const TestCase& test_case, const VCursor * cursor, uint32_t name_idx, uint32_t name_range_idx)
{
rc_t rc;
int64_t first_id;
uint64_t count_id;
rc = VCursorIdRange( cursor, name_idx, &first_id, &count_id );
if (rc != 0)
{
LOGERR( klogInt, rc, "VCursorIdRange() failed" );
return rc;
}
for (uint64_t row_id = first_id; row_id < first_id + count_id; ++row_id)
{
const char * name = NULL;
uint32_t name_len;
RowRange *row_range;
rc = VCursorCellDataDirect( cursor, row_id, name_idx, NULL, (void const **)&name, NULL, &name_len );
if ( rc != 0 )
return rc;
rc = VCursorParamsSet( ( struct VCursorParams const * )cursor, "QUERY_NAME", "%.*s", name_len, name );
if ( rc != 0 )
return rc;
rc = VCursorCellDataDirect( cursor, row_id, name_range_idx, NULL, (void const **)&row_range, NULL, NULL );
if ( rc != 0 )
return rc;
std::string name_str(name, name_len);
if (test_case.key_ranges.find(name_str) == test_case.key_ranges.end())
{
PLOGMSG( klogInt, (klogErr, "Unexpected name '$(NAME)' in test case '$(TC_NAME)'", "TC_NAME=%s,NAME=%s", test_case_name, name_str.c_str()) );
return 1;
}
RowRange row_range_exp = test_case.key_ranges.find(name_str)->second;
if (row_range->start_id != row_range_exp.start_id || row_range->stop_id != row_range_exp.stop_id)
{
PLOGMSG( klogInt, (klogErr, "Row range for name '$(NAME)' in test case '$(TC_NAME)' does not match. Expected: $(EXP_S)-$(EXP_F), actual: $(ACT_S)-$(ACT_F)",
"TC_NAME=%s,NAME=%s,EXP_S=%ld,EXP_F=%ld,ACT_S=%ld,ACT_F=%ld",
test_case_name, name_str.c_str(), row_range_exp.start_id, row_range_exp.stop_id, row_range->start_id, row_range->stop_id) );
return 1;
}
}
return rc;
}
/*
function INSDC:coord:zero NCBI:align:ref_pos ( I64 ref_id, INSDC:coord:zero ref_start );
*/
static
rc_t CC align_ref_pos ( void *data, const VXformInfo *info,
int64_t row_id, VRowResult *rslt, uint32_t argc, const VRowData argv[] )
{
rc_t rc = 0;
RefPos const *self = ( void const * )data;
int64_t ref_row_id = 0;
INSDC_coord_zero *ref_pos;
unsigned const ploidy = ( unsigned const )argv[ REF_START ].u.data.elem_count;
unsigned i;
/* get start and length of reference segment */
int64_t const *ref_id = 0;
INSDC_coord_zero const *ref_start;
assert( argv[ REF_ID ].u.data.elem_bits == sizeof( *ref_id ) * 8 );
assert( argv[ REF_START ].u.data.elem_bits == sizeof( *ref_start ) * 8 );
ref_start = argv[ REF_START ].u.data.base;
ref_start += argv[ REF_START ].u.data.first_elem;
if ( self->curs != NULL )
{
char const *name = NULL;
uint32_t name_len;
BSTRowRange *brr;
ref_id = argv[ REF_ID ].u.data.base;
ref_id += argv[ REF_ID ].u.data.first_elem;
brr = ( BSTRowRange * )BSTreeFind( &self->tr_range, &ref_id[ 0 ], row_range_cmp );
if ( brr == NULL )
{
RowRange *new_rr;
SUB_DEBUG( ( "SUB.Rd in 'align-ref-pos.c' at #%lu\n", ref_id[ 0 ] ) );
rc = VCursorCellDataDirect( self->curs, ref_id[ 0 ], self->name_idx, NULL, (void const **)&name, NULL, &name_len );
if ( rc != 0 )
return rc;
rc = VCursorParamsSet( ( struct VCursorParams const * )self->curs, "QUERY_SEQ_NAME", "%.*s", name_len, name );
if ( rc != 0 )
return rc;
rc = VCursorCellDataDirect( self->curs, ref_id[ 0 ], self->name_range_idx, NULL, (void const **)&new_rr, NULL, NULL );
if ( rc != 0 )
return rc;
brr = malloc( sizeof( *brr ) );
if ( brr == NULL )
{
return RC( rcXF, rcFunction, rcConstructing, rcMemory, rcExhausted );
}
else
{
memcpy( &brr->rr, new_rr, sizeof( *new_rr ) );
BSTreeInsert( ( BSTree* )&self->tr_range, ( BSTNode* )brr, row_range_sort );
}
}
ref_row_id = brr->rr.start_id;
}
rc = KDataBufferResize( rslt->data, ploidy );
if ( rc != 0 )
return rc;
ref_pos = rslt->data->base;
for ( i = 0; i != ploidy; ++i )
{
ref_pos[ i ] = ref_start[ i ];
if ( self->curs != NULL )
{
ref_pos[ i ] += ( INSDC_coord_zero )( ( ref_id[ 0 ] - ref_row_id ) * self->max_seq_len );
}
}
rslt->elem_count = ploidy;
rslt->elem_bits = sizeof( ref_pos[ 0 ] ) * 8;
return rc;
}
