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 [@property getter];

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

Properties

sequenceNames string[] sequenceNames [@property getter]: tbx.d: const(char **) tbx_seqnames(tbx_t *tbx, int *n); // free the array but not the values

Variables

fp htsFile* fp;: pointer to htsFile struct
header string header;: NGS flat file's header (if any; e.g. BED may not have one)
tbx tbx_t* tbx;: pointer to tabix handle

Meta

Source

See Implementation

dhtslib tabix structs

TabixIndexedFile