unit_test_vcfwriter.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <corelib/ncbiapp.hpp>
#include <corelib/ncbifile.hpp>
#include <connect/ncbi_core_cxx.hpp>
#include <serial/serial.hpp>
#include <serial/objistr.hpp>
#include <objmgr/object_manager.hpp>
#include <objmgr/scope.hpp>
#include <objmgr/seq_entry_ci.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/annot_ci.hpp>
#include <objtools/data_loaders/genbank/gbloader.hpp>
#include <dbapi/driver/drivers.hpp>
#include <objmgr/util/sequence.hpp>
#include <objtools/writers/writer_exception.hpp>
#include <objtools/writers/feature_context.hpp>
#include <objtools/writers/vcf_writer.hpp>
#include "error_logger.hpp"
#include <cstdio>
#include <corelib/test_boost.hpp>

Include dependency graph for unit_test_vcfwriter.cpp:

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Classes
struct	STestInfo
class	CTestNameToInfoMapLoader

Typedefs
typedef string	TTestName
typedef map< TTestName, STestInfo >	TTestNameToInfoMap

Functions
	USING_SCOPE (objects)
const string	extInput ("asn")
const string	extOutput ("vcf")
const string	extErrors ("errors")
const string	extKeep ("new")
const string	dirTestFiles ("vcfwriter_test_cases")
CVcfWriter *	sGetWriter (CScope &scope, CNcbiOstream &ostr)
void	sUpdateCase (CDir &test_cases_dir, const string &test_name)
void	sUpdateAll (CDir &test_cases_dir)
void	sRunTest (const string &sTestName, const STestInfo &testInfo, bool keep)
	NCBITEST_AUTO_INIT ()
	NCBITEST_INIT_CMDLINE (arg_descrs)
	NCBITEST_AUTO_FINI ()
	BOOST_AUTO_TEST_CASE (RunTests)

Variables
	USING_NCBI_SCOPE

Typedef Documentation

TTestName

typedef string TTestName

Definition at line 84 of file unit_test_vcfwriter.cpp.

TTestNameToInfoMap

typedef map<TTestName, STestInfo> TTestNameToInfoMap

Definition at line 85 of file unit_test_vcfwriter.cpp.

Function Documentation

BOOST_AUTO_TEST_CASE()

BOOST_AUTO_TEST_CASE

(

RunTests

)

Definition at line 340 of file unit_test_vcfwriter.cpp.

References CFile::Exists(), extErrors(), extInput(), extOutput(), fFF_Default, fFF_Recursive, FindFilesInDir(), CNcbiApplicationAPI::GetArgs(), CDirEntry::GetPath(), CNcbiApplication::Instance(), CDirEntry::IsDir(), ITERATE, STestInfo::mErrorFile, STestInfo::mInFile, STestInfo::mOutFile, sRunTest(), sUpdateAll(), and sUpdateCase().

dirTestFiles()

const string dirTestFiles

(

"vcfwriter_test_cases"

)

Referenced by NCBITEST_INIT_CMDLINE().

extErrors()

const string extErrors

(

"errors"

)

Referenced by BOOST_AUTO_TEST_CASE(), sUpdateAll(), and sUpdateCase().

extInput()

const string extInput

(

"asn"

)

Referenced by BOOST_AUTO_TEST_CASE(), sUpdateAll(), and sUpdateCase().

extKeep()

const string extKeep

(

"new"

)

Referenced by CTestNameToInfoMapLoader::operator()(), and sRunTest().

extOutput()

const string extOutput

(

"vcf"

)

Referenced by BOOST_AUTO_TEST_CASE(), sUpdateAll(), and sUpdateCase().

NCBITEST_AUTO_FINI()

NCBITEST_AUTO_FINI

(

)

Definition at line 336 of file unit_test_vcfwriter.cpp.

NCBITEST_AUTO_INIT()

NCBITEST_AUTO_INIT

(

)

Definition at line 314 of file unit_test_vcfwriter.cpp.

NCBITEST_INIT_CMDLINE()

NCBITEST_INIT_CMDLINE

(

arg_descrs

)

Definition at line 318 of file unit_test_vcfwriter.cpp.

References dirTestFiles(), CArgDescriptions::eDirectory, and CArgDescriptions::eString.

sGetWriter()

CVcfWriter* sGetWriter	(	CScope &	scope,
		CNcbiOstream &	ostr
	)

Definition at line 166 of file unit_test_vcfwriter.cpp.

Referenced by sRunTest(), and sUpdateCase().

sRunTest()

void sRunTest	(	const string &	sTestName,
		const STestInfo &	testInfo,
		bool	keep
	)

Definition at line 246 of file unit_test_vcfwriter.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), CFile::CompareTextContents(), CDirEntry::Copy(), CFile::eIgnoreWs, eSerial_AsnText, extKeep(), CObjectManager::GetInstance(), CDirEntry::GetName(), CDirEntry::GetPath(), CDirEntry::GetTmpName(), STestInfo::mErrorFile, STestInfo::mInFile, STestInfo::mObjType, STestInfo::mOutFile, CObjectIStream::Open(), CGBDataLoader::RegisterInObjectManager(), CDirEntry::Remove(), sGetWriter(), CVcfWriter::WriteAnnot(), CWriterBase::WriteFooter(), CWriterBase::WriteHeader(), and CWriterBase::WriteSeqEntryHandle().

Referenced by BOOST_AUTO_TEST_CASE().

sUpdateAll()

void sUpdateAll

(

CDir &

test_cases_dir

)

Definition at line 224 of file unit_test_vcfwriter.cpp.

References extErrors(), extInput(), extOutput(), fFF_Default, fFF_Recursive, FindFilesInDir(), ITERATE, and sUpdateCase().

Referenced by BOOST_AUTO_TEST_CASE().

sUpdateCase()

void sUpdateCase	(	CDir &	test_cases_dir,
		const string &	test_name
	)

Definition at line 171 of file unit_test_vcfwriter.cpp.

References CScope::AddDefaults(), CScope::AddTopLevelSeqEntry(), CDirEntry::ConcatPath(), eSerial_AsnText, extErrors(), extInput(), extOutput(), CObjectManager::GetInstance(), CDirEntry::GetPath(), input(), CObjectIStream::Open(), output, CGBDataLoader::RegisterInObjectManager(), sGetWriter(), NStr::SplitInTwo(), test_name, test_type(), CVcfWriter::WriteAnnot(), CWriterBase::WriteFooter(), CWriterBase::WriteHeader(), and CWriterBase::WriteSeqEntryHandle().

Referenced by BOOST_AUTO_TEST_CASE(), and sUpdateAll().

USING_SCOPE()

USING_SCOPE

(

objects

)

Variable Documentation

USING_NCBI_SCOPE

USING_NCBI_SCOPE

Definition at line 63 of file unit_test_vcfwriter.cpp.