VCFWriter

Constructors

this

this()

Undocumented in source.

this

this(string fn)

open file or network resources for writing setup incl header allocation if mode==w: bcf_hdr_init automatically sets version string (##fileformat=VCFv4.2) bcf_hdr_init automatically adds the PASS filter

this

this(string fn, T other)

setup and copy a header from another BCF/VCF as template

Members

Functions

addFiledate

deprecated int addFiledate()

Undocumented in source. Be warned that the author may not have intended to support it.

addFilterTag

deprecated void addFilterTag(string id, string description)

Add FILTER tag (§1.2.3)

addHeaderLineKV

deprecated int addHeaderLineKV(string key, string value)

Undocumented in source. Be warned that the author may not have intended to support it.

addHeaderLineRaw

deprecated int addHeaderLineRaw(string line)

Undocumented in source. Be warned that the author may not have intended to support it.

addRecord

int addRecord(S contig, int pos, S id, S alleles, N qual, S[] filters)

Add a record

addSample

deprecated int addSample(string name)

Add sample to this VCF * int bcf_hdr_add_sample(bcf_hdr_t *hdr, const(char) *sample);

addTag

deprecated void addTag(string id, HeaderLengths number, HeaderTypes type, string description, string source, string _version)

Add INFO (§1.2.2) or FORMAT (§1.2.4) tag

addTag

deprecated void addTag(string id, string description)

Add FILTER tag (§1.2.3)

addTag

deprecated auto addTag(const(char)[] id, int length, string other)

Add contig definition (§1.2.7) to header meta-info

getHeader

VCFHeader getHeader()

Undocumented in source. Be warned that the author may not have intended to support it.

writeHeader

int writeHeader()

as expected

writeRecord

int writeRecord(VCFRecord r)

as expected

writeRecord

int writeRecord(bcf_hdr_t* hdr, bcf1_t* rec)

as expected

Variables

fp

VcfFile fp;

rc htsFile wrapper

rows

Bcf1[] rows;

individual records

vcfhdr

VCFHeader vcfhdr;

header wrapper

import std.exception: assertThrown;
import std.stdio: writeln, writefln;
import dhtslib.vcf.writer;

hts_set_log_level(htsLogLevel.HTS_LOG_TRACE);


auto vw = VCFWriter("/dev/null");

vw.addHeaderLineRaw("##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of Samples With Data\">");
vw.addHeaderLineKV("INFO", "<ID=DP,Number=1,Type=Integer,Description=\"Total Depth\">");
// ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">
vw.addTag!(HeaderRecordType.Info)("AF", HeaderLengths.OnePerAltAllele, HeaderTypes.Integer, "Number of Samples With Data");
vw.addTag!(HeaderRecordType.Filter)("filt","test");
vw.addFilterTag("filt2","test2");

assert(vw.getHeader.getHeaderRecord(HeaderRecordType.Filter, "filt2").getDescription == "\"test2\"");
vw.writeHeader();

• BCFWriter

• VCFWriter