TabixIndexedFile

Encapsulates a position-sorted record-oriented NGS flat file, indexed with Tabix, including BED, GFF3, VCF.

region(string r) returns an InputRange that iterates through rows of the file intersecting or contained within the requested range

struct TabixIndexedFile {

string header;

this(const(char)[] fn, const(char)[] fntbi);

string[] sequenceNames();

auto region(const(char)[] r);

}

Constructors

this this(const(char)[] fn, const(char)[] fntbi): Initialize with a complete file path name to the tabix-indexed file The tabix index (.tbi) must already exist alongside

Destructor

~this ~this(): Undocumented in source.

Members

Functions

region auto region(const(char)[] r): region(r) returns an InputRange that iterates through rows of the file intersecting or contained within the requested range
sequenceNames string[] sequenceNames(): tbx.d: const(char **) tbx_seqnames(tbx_t *tbx, int *n); // free the array but not the values

Variables

fp htsFile* fp;: Undocumented in source.
header string header;: Undocumented in source.
tbx tbx_t* tbx;: Undocumented in source.

Meta

Source

See Implementation

dhtslib tabix structs

TabixIndexedFile