tile_summary.h
Go to the documentation of this file.
26 void update_extended_tile_summary_from_cache(std::vector<ExtendedTileVector>& extended_tile_data,
110 inline size_t update_read_summary(summary_by_lane_read<model::metrics::read_metric>::vector_t& read_data_cache,
188 summary_by_lane_read<model::metrics::read_metric> read_data_by_surface_lane_read(run, n, surface_count);
195 INTEROP_BOUNDS_CHECK(lane, tile_data_by_lane.size(), "Lane exceeds number of lanes in RunInfo.xml");
196 tile_data_by_lane[beg->lane() - 1].push_back(*beg);// TODO: make more efficient by copying only tile data
197 for (const_read_metric_iterator rb = beg->read_metrics().begin(), re = beg->read_metrics().end();
201 INTEROP_BOUNDS_CHECK(read, read_data_by_lane_read.read_count(), "Read exceeds number of reads in RunInfo.xml");
208 tile_data_by_lane_surface[index].push_back(*beg);// TODO: make more efficient by copying only tile data
304 run.nonindex_summary().percent_aligned(divide(percent_aligned_nonindex, static_cast<float>(total_nonindex)));
348 INTEROP_BOUNDS_CHECK(lane, tile_data_by_lane.size(), "Lane exceeds number of lanes in RunInfo.xml");
349 tile_data_by_lane[beg->lane() - 1].push_back(*beg);// TODO: make more efficient by copying only tile data
352 tile_data_by_lane_surface[index].push_back(*beg);// TODO: make more efficient by copying only tile data
366 tile_vector_t::iterator tile_lane_end = util::remove_nan(tile_lane_data.begin(), tile_lane_data.end(),
367 util::op::const_member_function(&model::metrics::extended_tile_metric::cluster_count_occupied));
389 update_extended_tile_summary_from_cache(tile_data_by_lane_surface[lane * surface_count + surface],
400 run[read].summary().percent_occupied(static_cast<float>(divide(total_cluster_occupied, total_cluster_count))*100);
402 run.nonindex_summary().percent_occupied(static_cast<float>(divide(total_cluster_occupied, total_cluster_count))*100);
403 run.total_summary().percent_occupied(static_cast<float>(divide(total_cluster_occupied, total_cluster_count))*100);
void update_extended_tile_summary_from_cache(std::vector< ExtendedTileVector > &extended_tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)
Definition: tile_summary.h:26
const metric_summary & total_summary() const
Definition: run_summary.h:314
const metric_stat_t & cluster_count_pf() const
Definition: stat_summary.h:138
Definition: enum_description.h:15
float cluster_count() const
Definition: tile_metric.h:334
size_t surface_count() const
Definition: run_summary.h:287
const metric_stat_t & prephasing() const
Definition: stat_summary.h:165
float percent_prephasing() const
Definition: tile_metric.h:126
float percent_aligned() const
Definition: metric_summary.h:60
std::vector< read_metric > read_metric_vector
Definition: tile_metric.h:177
S nan_accumulate(I beg, I end, const S init, Op op)
Definition: summary_statistics.h:209
inline::uint32_t surface(const ::uint32_t tile_id, const constants::tile_naming_method method)
Definition: tile_metric.h:93
size_t size() const
Definition: run_summary.h:224
float cluster_density() const
Definition: tile_metric.h:306
void summarize_extended_tile_metrics(I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run)
Definition: tile_summary.h:326
const metric_stat_t & percent_pf() const
Definition: stat_summary.h:147
float percent_phasing() const
Definition: tile_metric.h:118
float cluster_count_pf() const
Definition: tile_metric.h:355
const metric_stat_t & density() const
Definition: stat_summary.h:111
const_member_function_less_w< T, R, P1 > const_member_function_less(const P2 ¶m1, R(T::*func)(P1) const)
Definition: statistics.h:233
size_t nan_summarize(I beg, I end, S &stat, BinaryOp op, Compare comp, const bool skip_median)
Definition: summary_statistics.h:187
const_member_function_w< T, R, P1 > const_member_function(const P2 ¶m1, R(T::*func)(P1) const)
Definition: statistics.h:197
float percent_occupied() const
Definition: extended_tile_metric.h:129
def summary(run_metrics, level='Total', columns=None, dtype='f4', ignore_missing_columns=True, extra)
Definition: core.py:217
void reserve(I beg, I end, const ptrdiff_t n)
Definition: summary_statistics.h:24
const metric_stat_t & percent_occupied() const
Definition: stat_summary.h:278
float percent_pf() const
Definition: tile_metric.h:376
double cluster_count() const
Definition: metric_summary.h:125
def read(run, valid_to_load=None, requires=None, search_paths=None, extra)
Definition: core.py:752
float cluster_density_pf() const
Definition: tile_metric.h:320
void summarize_tile_metrics(I beg, I end, const constants::tile_naming_method naming_method, model::summary::run_summary &run, const bool skip_median=false)
Definition: tile_summary.h:165
Definition: run_summary.h:23
float cluster_count_occupied() const
Definition: extended_tile_metric.h:107
Definition: stat_summary.h:24
I remove_nan(I beg, I end, UnaryOp op)
Definition: statistics.h:479
uint64_t reads_pf() const
Definition: metric_summary.h:150
std::vector< T > vector_t
Definition: summary_statistics.h:36
uint64_t reads() const
Definition: metric_summary.h:142
const metric_stat_t & density_pf() const
Definition: stat_summary.h:120
Definition: metric_exceptions.h:25
const metric_stat_t & percent_aligned() const
Definition: stat_summary.h:174
uint64_t reads() const
Definition: stat_summary.h:92
size_t update_read_summary(summary_by_lane_read< model::metrics::read_metric >::vector_t &read_data_cache, model::summary::stat_summary &stat_summary, const bool skip_median)
Definition: tile_summary.h:110
const metric_stat_t & phasing() const
Definition: stat_summary.h:156
const metric_stat_t & cluster_count() const
Definition: stat_summary.h:129
Definition: metric_stat.h:16
uint64_t reads_pf() const
Definition: stat_summary.h:101
float percent_aligned() const
Definition: tile_metric.h:110
size_t lane_count() const
Definition: run_summary.h:270
void update_tile_summary_from_cache(std::vector< TileVector > &tile_data, model::summary::stat_summary &stat_summary, const bool skip_median)
Definition: tile_summary.h:48
double cluster_count_pf() const
Definition: metric_summary.h:134
float divide(const float num, const float div)
Definition: summary_statistics.h:231
Definition: summary_statistics.h:32
const metric_summary & nonindex_summary() const
Definition: run_summary.h:342