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(string chrom, Interval!cs coords);

}

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

Members

Functions

region auto region(string chrom, Interval!cs coords): 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;: rc wrapper around htsFile ptr
header string header;: NGS flat file's header (if any; e.g. BED may not have one)
tbx Tbx tbx;: rc wrapper around tabix ptr

Meta

Source

See Implementation

dhtslib tabix structs