VCFReaderImpl

Basic support for reading VCF, BCF files

struct VCFReaderImpl (

bool isTabixFile

) {

VCFHeader vcfhdr;

UnpackLevel MAX_UNPACK;

static if(isTabixFile)

TabixIndexedFile tbx;

static if(isTabixFile)

ReturnType!(this.initializeTabixRange) tbxRange;

this(TabixIndexedFile tbxFile, string chrom, Interval!cs coords, UnpackLevel MAX_UNPACK);

static if(isTabixFile)

auto initializeTabixRange(string chrom, Interval!cs coords);

this(string fn, UnpackLevel MAX_UNPACK);

VCFHeader getHeader();

bool empty [@property getter];

void popFront();

VCFRecord front();

typeof(this) save();

}

Constructors

this this(): Undocumented in source.
this this(TabixIndexedFile tbxFile, string chrom, Interval!cs coords, UnpackLevel MAX_UNPACK): TabixIndexedFile and coordinates ctor
this this(string fn, UnpackLevel MAX_UNPACK): read existing VCF file

Members

Functions

front VCFRecord front(): InputRange interface: iterate over all records
getHeader VCFHeader getHeader(): Undocumented in source. Be warned that the author may not have intended to support it.
initializeTabixRange auto initializeTabixRange(string chrom, Interval!cs coords): copy the TabixIndexedFile.region range
popFront void popFront(): InputRange interface: iterate over all records
save typeof(this) save(): Undocumented in source. Be warned that the author may not have intended to support it.

Properties

empty bool empty [@property getter]: InputRange interface: iterate over all records

Variables

MAX_UNPACK UnpackLevel MAX_UNPACK;: see htslib.vcf
b Bcf1 b;: rc bcf1_t wrapper, record for use in iterator, will be recycled
fp VcfFile fp;: rc htsFile wrapper
tbx TabixIndexedFile tbx;: For tabix use
tbxRange ReturnType!(this.initializeTabixRange) tbxRange;: For tabix use
vcfhdr VCFHeader vcfhdr;: rc header wrapper

Meta

Source

See Implementation

dhtslib vcf reader aliases

BCFReader

functions

VCFReader

structs

VCFReaderImpl