bioh5g_alignment_data Struct Reference

Alignment data container. More...

#include <bioh5g_alignments.h>

Data Fields
int64_t	read_index
	The HDF5 index/offset for the associated read.
char *	reference
	The reference name.
int32_t	position
	The position on the reference (left endpoint, 1-based inclusive)
int32_t	length
	The length of the alignment.
unsigned char	sam_mapq
	SAM quality (MAPQ) value.
int32_t	sam_flags
	The SAM FLAGS.
char *	sam_cigar
	The SAM CIGAR string.
char *	sam_tags
	The SAM tag string.
char *	sam_rnext
	The reference of the next alignment in the template.
int32_t	sam_pnext
	The position of the next alignment in the template.
int32_t	sam_tlen
	The template length.

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Detailed Description

Alignment data container.

Currently very SAM-centric but will be made more generic in the future.

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

• bioh5g_alignments.h