static rc_t read_loop( statistic * data,
context *ctx,
statistic_reader *reader,
const VCursor *my_cursor )
{
int64_t first;
uint64_t count;
rc_t rc = query_reader_rowrange( reader, &first, &count );
if ( rc != 0 )
LogErr( klogInt, rc, "query_statistic_rowrange() failed\n" );
else
{
if ( num_gen_empty( ctx->row_generator ) )
{
rc = num_gen_add( ctx->row_generator, first, count );
if ( rc != 0 )
LogErr( klogInt, rc, "num_gen_add() failed() failed\n" );
}
else
{
rc = num_gen_trim( ctx->row_generator, first, count );
if ( rc != 0 )
LogErr( klogInt, rc, "num_gen_trim() failed() failed\n" );
}
if ( rc == 0 )
{
const num_gen_iter *iter;
rc = num_gen_iterator_make( ctx->row_generator, &iter );
if ( rc != 0 )
LogErr( klogInt, rc, "num_gen_iterator_make() failed\n" );
else
{
uint64_t row_id;
progressbar * progress;
rc = make_progressbar( &progress );
if ( rc != 0 )
LogErr( klogInt, rc, "make_progressbar() failed\n" );
else
{
uint8_t fract_digits = calc_fract_digits( iter );
uint32_t percent;
row_input row_data;
while ( ( num_gen_iterator_next( iter, &row_id ) == 0 )&&
( rc == 0 ) )
{
rc = Quitting();
if ( rc == 0 )
{
/* ******************************************** */
rc = reader_get_data( reader, &row_data, row_id );
if ( rc == 0 )
{
rc = extract_statistic_from_row( data, &row_data, row_id );
}
/* ******************************************** */
if ( ctx->show_progress )
if ( num_gen_iterator_percent( iter, fract_digits, &percent ) == 0 )
update_progressbar( progress, fract_digits, percent );
}
}
destroy_progressbar( progress );
if ( ctx->show_progress )
OUTMSG(( "\n" ));
}
num_gen_iterator_destroy( iter );
}
}
}
return rc;
}
static
rc_t CC qstats_trigger_impl(void *data, const VXformInfo *info, int64_t row_id,
VRowResult *rslt, uint32_t argc, const VRowData argv[])
{
self_t *self = data;
unsigned const nreads = argv[2].u.data.elem_count;
unsigned nrofs = 0;
unsigned i;
unsigned start;
rc_t rc = 0;
uint8_t const *read = argv[0].u.data.base;
uint8_t const *qual = argv[1].u.data.base;
uint32_t const *rlen = argv[2].u.data.base;
INSDC_SRA_xread_type const *rtyp = argv[3].u.data.base;
char const *sgrp = argv[4].u.data.base;
bool const *hmis = NULL;
bool const *hrof = NULL;
int32_t const *rofs = NULL;
read += argv[0].u.data.first_elem;
qual += argv[1].u.data.first_elem;
rlen += argv[2].u.data.first_elem;
rtyp += argv[3].u.data.first_elem;
sgrp += argv[4].u.data.first_elem;
if (argc > 5) {
hmis = argv[5].u.data.base;
hmis += argv[5].u.data.first_elem;
hrof = argv[6].u.data.base;
hrof += argv[6].u.data.first_elem;
rofs = argv[7].u.data.base;
rofs += argv[7].u.data.first_elem;
nrofs = argv[7].u.data.elem_count;
}
for (start = i = 0; i < nreads && rc == 0; ++i) {
row_input row;
unsigned const len = rlen[i];
memset(&row, 0, sizeof(row));
row.spotgroup = sgrp;
row.spotgroup_len = argv[4].u.data.elem_count;
row.read = &read[start];
row.quality = &qual[start];
row.read_len = row.quality_len = len;
row.reversed = (rtyp[i] & SRA_READ_TYPE_REVERSE) != 0;
row.base_pos_offset = start;
start += len;
if (hmis) {
row.has_mismatch = hmis;
row.has_roffs = hrof;
row.roffs = rofs;
row.has_mismatch_len = row.has_roffs_len = len;
row.roffs_len = nrofs;
}
rc = extract_statistic_from_row(&self->stats, &row);
}
return rc;
}
