ngs Namespace Reference

Typedefs
typedef std::vector< Alignment * >	AlignmentVector
typedef std::vector< std::string >	StringVector

Functions
void	readVCF (const AlignmentVector &sources, const StringVector &filenames, const float minQuality, const float minCoverage, const bool ignoreFilter, const char *const replacementChar)

Typedef Documentation

AlignmentVector

typedef std::vector<Alignment *> ngs::AlignmentVector

Definition at line 44 of file VCFHandler.h.

StringVector

typedef std::vector<std::string> ngs::StringVector

Definition at line 45 of file VCFHandler.h.

Function Documentation

readVCF()

void ngs::readVCF	(	const AlignmentVector &	sources,
		const StringVector &	filenames,
		const float	minQuality,
		const float	minCoverage,
		const bool	ignoreFilter,
		const char *const	replacementChar
	)

Parameters

[in,out]	sources	List of Alignments, each of them having one sequence, the reference one. They fill be extended with one sequence for each donor found on the VCF dataset, and their SNP will be applied to the correspondent sequence.
[in]	filenames	List of VCF files to parse and apply.
[in]	minQuality	Min quality a SNP should have to be applied.
[in]	minCoverage	Min coverage a SNP should have to be applied.
[in]	ignoreFilter	Whether to ignore filter field in VCF
[in]	replacementChar	Replacement char to apply when VCF-feature doesn't pass the filter.

Definition at line 619 of file VCFHandler.cpp.

Referenced by trimAlManager::perform().

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