#include <ncbi_pch.hpp>
#include <thread>
#include <gui/widgets/loaders/columnar_vcf_cache.hpp>
#include <gui/widgets/loaders/columnar_vcf_variants_base.hpp>
#include <gui/widgets/loaders/report_loader_errors.hpp>
#include <gui/widgets/loaders/columnar_vcf_reader.hpp>
#include <gui/widgets/loaders/columnar_vcf_variants.hpp>
#include <gui/widgets/wx/compressed_file.hpp>
#include <connect/ncbi_conn_exception.hpp>
#include <corelib/perf_log.hpp>
#include <corelib/ncbireg.hpp>
#include <corelib/ncbistr.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objtools/readers/line_error.hpp>
#include <util/md5.hpp>

Include dependency graph for columnar_vcf_cache.cpp:

Go to the SVN repository for this file.

Namespaces
	ColumnarVcfCache

Functions
	USING_SCOPE (objects)

bool	ColumnarVcfCache::CreateBlob (const std::string &url, const std::string &id, CColumnarVcfCache &cache, size_t &blob_size, TReportError report_error, const unsigned retries_count=1, bool enforce_size_limit=true)
	Creates a VCF blob for a given scaffold id and VCF url. More...

void	ColumnarVcfCache::ReportSyntaxErrors (CErrorContainer *err_cont)
	Reports VCF syntax errors to AppLog. More...

void	ColumnarVcfCache::SetInfoFields (set< string > &fields)
	Get the list of INFO fields to read. More...

Variables
static const string	kVcfCacheBlob = "VcfBlobsCache"

static const string	kVcfCacheSync = "VcfSyncCache"

const unsigned	s_MaxVarsPerCHR { 2000 }

Function Documentation

◆ USING_SCOPE()

USING_SCOPE ( objects )

Variable Documentation

◆ kVcfCacheBlob

const string kVcfCacheBlob = "VcfBlobsCache"

static

Definition at line 58 of file columnar_vcf_cache.cpp.

Referenced by CColumnarVcfCache::x_InitBlobCache().

◆ kVcfCacheSync

const string kVcfCacheSync = "VcfSyncCache"

static

Definition at line 59 of file columnar_vcf_cache.cpp.

Referenced by CColumnarVcfCache::x_InitSyncCache().

◆ s_MaxVarsPerCHR

const unsigned s_MaxVarsPerCHR { 2000 }

Definition at line 60 of file columnar_vcf_cache.cpp.

Referenced by ColumnarVcfCache::CreateBlob().

Namespaces