SAM/BAM file IO. More...

Classes
class	shore::sam_base
	Shared functionality for sam_reader and bam_reader. More...

struct	shore::sam_base::config
	Configuration struct that may be passed to sam_reader or bam_reader. More...

class	shore::sam_reader
	Reader for SAM alignment files. More...

class	shore::bam_reader
	Reader for BAM alignment files. More...

class	shore::sam_writer
	Writer for SAM alignment files. More...

Typedefs
typedef shore::source< sam_reader >	shore::sam_source
	SAM file pipeline source.

typedef shore::source< bam_reader >	shore::bam_source
	BAM file pipeline source.

typedef shore::sink< sam_writer >	shore::sam_sink
	SAM file pipeline sink.

typedef shore::sink < sam_writer, shore::read >	shore::sam_read_sink
	SAM file pipeline sink for unaligned reads.

Enumerations
enum	shore::SAMFlags { SAM_PE_PAIRED_END =0x001, SAM_PE_PROPER_PAIR =0x002, SAM_UNMAPPED_SELF =0x004, SAM_PE_UNMAPPED_MATE =0x008, SAM_REVERSE_SELF =0x010, SAM_REVERSE_MATE =0x020, SAM_PE_READ1 =0x040, SAM_PE_READ2 =0x080, SAM_NO_PRIMARY_ALIGNMENT =0x100, SAM_QUALITY_FILTERED =0x200, SAM_DUPLICATE_READ =0x400 }
	Enumeration of valid SAM flags (bitmask).

Detailed Description

SAM/BAM file IO.

Classes