VCFReaderImpl

Constructors

this

this()

Undocumented in source.

this

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

TabixIndexedFile and coordinates ctor

this

this(string fn, int extra_threads, UnpackLevel MAX_UNPACK)

read existing VCF file

Postblit

this(this)

this(this)

Explicit postblit to avoid https://github.com/blachlylab/dhtslib/issues/122

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

• BCFReader

• VCFReader

• VCFReaderImpl