rc_t extract_statistic_from_row( statistic * data,
row_input * row_data,
const int64_t row_id )
{
rc_t rc = 0;
spotgrp *sg;
/* first try the SPOT_GROUP column (correct for newer db's) */
char * spotgrp_base = row_data->spotgroup;
uint32_t spotgrp_len = row_data->spotgroup_len;
/* first try the SPOT_GROUP column (correct for newer db's) */
if ( spotgrp_len < 1 || *spotgrp_base == 0 )
{
/* if empty try with SEQ_SPOT_GROUP column (correct for older db's) */
spotgrp_base = row_data->seq_spotgroup;
spotgrp_len = row_data->seq_spotgroup_len;
}
sg = find_spotgroup( data, spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
sg = make_spotgrp( spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
rc = RC( rcApp, rcSelf, rcConstructing, rcMemory, rcExhausted );
PLOGERR( klogInt, ( klogInt, rc,
"make_spotgrp failed at row $(row_nr)", "row_nr=%lu", row_id ) );
}
else
{
rc = BSTreeInsert ( &data->spotgroups, (BSTNode *)sg, spotgroup_sort );
if ( rc != 0 )
{
PLOGERR( klogInt, ( klogInt, rc,
"BSTreeInsert( new spotgroup ) at row $(row_nr)", "row_nr=%lu", row_id ) );
}
}
}
if ( rc == 0 )
{
uint32_t n_bases = row_data->read_len;
if ( ( n_bases == row_data->quality_len ) &&
( n_bases == row_data->has_mismatch_len ) )
{
rc = extract_spotgroup_statistic( data, sg, n_bases, row_data, row_id );
}
else
{
rc = RC( rcApp, rcNoTarg, rcConstructing, rcData, rcInvalid );
PLOGERR( klogInt, ( klogInt, rc,
"number of bases, quality and has_mismatch is not the same at row $(row_nr)",
"row_nr=%lu", row_id ) );
}
}
return rc;
}
rc_t extract_statistic_from_row(statistic *self,
row_input const *data)
{
rc_t rc = 0;
spotgrp *sg;
char const *spotgrp_base;
uint32_t spotgrp_len;
unsigned i;
uint8_t lb = 4;
unsigned hpr = 0;
unsigned gcc = 0;
if (data == NULL) {
return RC(rcXF, rcFunction, rcExecuting, rcParam, rcNull);
}
if (self == NULL) {
return RC(rcXF, rcFunction, rcExecuting, rcSelf, rcNull);
}
rc = validate_row_data(self, data);
if (rc)
return rc;
spotgrp_base = data->spotgroup;
spotgrp_len = data->spotgroup_len;
if (spotgrp_base == NULL || spotgrp_len == 0) {
spotgrp_base = "";
spotgrp_len = 0;
}
sg = find_spotgroup( self, spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
sg = make_spotgrp( spotgrp_base, spotgrp_len );
if ( sg == NULL )
{
return RC( rcXF, rcFunction, rcExecuting, rcMemory, rcExhausted );
}
else
{
rc = BSTreeInsert ( &self->spotgroups, (BSTNode *)sg, spotgroup_sort );
if (rc)
return rc;
}
}
for (i = 0; i < data->read_len && rc == 0; ++i) {
unsigned const base = data->read[i];
unsigned dimer;
if (base > 3) {
dimer = 16;
hpr = 0;
}
else {
dimer = (lb > 3) ? 16 : ((lb << 2) | base);
if (lb == base)
++hpr;
else
hpr = 0;
}
if (i > 0)
rc = spotgroup_enter_values(sg, data->quality[i], dimer, gcc, hpr, data->base_pos_offset + i, CASE_MATCH);
if (base == 1 || base == 2)
++gcc;
if (i >= self->gc_window) {
unsigned const out = data->read[i - self->gc_window];
if (out == 1 || out == 2)
--gcc;
}
lb = base;
}
return rc;
}
