cgatools::mapping::SamGeneratorConfig Class Reference

Sam Generator configuration parameters. More...

#include <SamOptions.hpp>

List of all members.

Public Attributes
bool	mateSvCandidates_
bool	addMateSequenceAndScore_
bool	addMateSequenceAndScoreIfMateUnmapped_
bool	printAlleleInfo_
bool	packCigar_
	if packed the cigar looses information about 0-sized gaps but does not cause format errors in GATK
bool	addAlternativeMates_
bool	addAlternativeMappings_
bool	skipNotMapped_
bool	primaryMappingsOnly_
int	maxConsistentRange_

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Detailed Description

Sam Generator configuration parameters.

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The documentation for this class was generated from the following file:

• SamOptions.hpp