Writer for SAM alignment files. More...

Public Types
enum	SamSorting { SAM_SO_UNKNOWN, SAM_SO_UNSORTED, SAM_SO_COORDINATE, SAM_SO_QUERYNAME }

typedef shore::alignment	append_type

Public Member Functions
	sam_writer (const std::string &fn, const std::vector< std::string > &allowed_readgroups)

	sam_writer (std::ostream *const os, const std::vector< std::string > &allowed_readgroups)

void	write_header (const std::string &fasta_fn=std::string(), const SamSorting sort=SAM_SO_UNKNOWN)
	Write SAM header for the given reference sequence file and the given SAM sorting.

void	set_correct_leftover_flags (const bool b)
	Store orphan mapping positions and read IDs to correctly set the SAM flags for later appended leftover reads.

void	set_orphan_leftovers_only (const bool b)
	Set if only those leftover reads should be written whose partners are mapping orphans.

void	append (const shore::alignment &f)

void	append (const shore::read &f)

void	flush ()

Detailed Description

Writer for SAM alignment files.

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

Public Types