VCFWriter

Basic support for writing VCF, BCF files

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

Destructor

~this ~this(): dtor

Members

Functions

addFiledate int addFiledate(): Add a filedate= headerline, which is not called out specifically in the spec, but appears in the spec's example files. We could consider allowing a param here.
addFilterTag deprecated void addFilterTag(string id, string description): Add FILTER tag (§1.2.3)
addHeaderLineKV int addHeaderLineKV(string key, string value): Add a new header line
addHeaderLineRaw int addHeaderLineRaw(string line): Add a new header line -- must be formatted ##key=value
addRecord int addRecord(S contig, int pos, S id, S alleles, N qual, S[] filters): Add a record
addSample int addSample(string name): Add sample to this VCF * int bcf_hdr_add_sample(bcf_hdr_t *hdr, const(char) *sample);
addTag void addTag(string id, T number, string type, string description, string source, string _version): Add INFO (§1.2.2) or FORMAT (§1.2.4) tag
addTag void addTag(string id, string description): Add FILTER tag (§1.2.3)
addTag auto addTag(const(char)[] id, int length, string other): Add contig definition (§1.2.7) to header meta-info
copyHeaderLines void copyHeaderLines(bcf_hdr_t* other): copy header lines from a template without overwiting existing lines
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;: htsFile
rows bcf1_t*[] rows;: individual records
vcfhdr VCFHeader* vcfhdr;: header wrapper -- no copies

VCFWriter

Constructors

Destructor

Members

Functions

Variables

Meta

Source