VCFRecord

Wrapper around bcf1_t

Because it uses bcf1_t internally, it must conform to the BCF2 part of the VCFv4.2 specs, rather than the loosey-goosey VCF specs. i.e., INFO, CONTIG, FILTER records must exist in the header.

TODO: Does this need to be kept in a consistent state? Ideally, VCFWriter would reject invalid ones, but we are informed that it is invalid (e.g. if contig not found) while building this struct; bcf_write1 will actually segfault, unfortunately. I'd like to avoid expensive validate() calls for every record before writing if possible, which means keeping this consistent. However, not sure what to do if error occurs when using the setters herein?

2019-01-23 struct->class to mirror SAMRecord -- faster if reference type?

2019-01-23 WIP: getters for chrom, pos, id, ref, alt are complete (untested)

After parsing a BCF or VCF line, bcf1_t must be unpacked. (not applicable when building bcf1_t from scratch) Depending on information needed, this can be done to various levels with performance tradeoff. Unpacking symbols:

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class VCFRecord {

bcf1_t* line;

VCFHeader* vcfheader;

this(T* h, bcf1_t* b, int MAX_UNPACK);

this(VCFHeader* vcfhdr, string chrom, int pos, string id, string _ref, string alt, float qual, SS filter);

this(VCFHeader* vcfhdr, string line, int MAX_UNPACK);

~this();

string chrom [@property getter];

const(char)[] chrom [@property setter];

int pos [@property getter];

int pos [@property setter];

string id [@property getter];

const(char)[] id [@property setter];

int addID(const(char)[] id);

int refLen [@property getter];

string[] allelesAsArray [@property getter];

string refAllele [@property getter];

string[] altAllelesAsArray [@property getter];

string altAllelesAsString [@property getter];

string alleles [@property setter];

string[] alleles [@property setter];

void setRefAllele(const(char)* r);

void setAlleles(string _ref, string alt);

void setAlleles(string _ref, string alt, ...);

float qual [@property getter];

float qual [@property setter];

string filter [@property getter];

void removeAllFilters();

string filter [@property setter];

string[] filter [@property setter];

int addFilter(string f);

int removeFilter(string f);

int removeFilter(int fid);

bool hasFilter(string filter);

void addInfo(string tag, T data);

void addInfo(string tag, T[] data);

void addFormat(string tag, T data);

void addFormat(string tag, T[] data);

void add(const(char)[] tag, T data);

string toString();

}

Constructors

this this(T* h, bcf1_t* b, int MAX_UNPACK)
this(VCFHeader* vcfhdr, string chrom, int pos, string id, string _ref, string alt, float qual, SS filter)
this(VCFHeader* vcfhdr, string line, int MAX_UNPACK): VCFRecord

Destructor

~this ~this(): disable copying to prevent double-free (which should not come up except when writeln'ing) dtor

Members

Functions

add void add(const(char)[] tag, T data): add INFO or FORMAT key:value pairs to a record add a single datapoint OR vector of values, OR, values to each sample (if tagType == FORMAT)
addFilter int addFilter(string f): Add a filter; from htslib: "If flt_id is PASS, all existing filters are removed first. If other than PASS, existing PASS is removed."
addFormat void addFormat(string tag, T[] data): auto bcf_update_format_int32(const(bcf_hdr_t) *hdr, bcf1_t *line, const(char) *key, int *values, int n) // @suppress(dscanner.style.undocumented_declaration)
addFormat void addFormat(string tag, T data): bc_update_format_{int32,flat,string,flag}
addID int addID(const(char)[] id): Append an ID (htslib performs duplicate checking)
addInfo void addInfo(string tag, T data): Add a tag:value to the INFO column -- tag must already exist in the header
addInfo void addInfo(string tag, T[] data): ditto This handles a vector of values for the tag
hasFilter bool hasFilter(string filter): Determine whether FILTER is present. log warning if filter does not exist. "PASS" and "." can be used interchangeably.
removeAllFilters void removeAllFilters(): Remove all entries in FILTER
removeFilter int removeFilter(string f): Remove a filter by name
removeFilter int removeFilter(int fid): Remove a filter by numeric id
setAlleles void setAlleles(string _ref, string alt): Set alleles; alt can be comma separated
setAlleles void setAlleles(string _ref, string alt, ...): Set alleles; min. 2 alleles (ref, alt1); unlimited alts may be specified
setRefAllele void setRefAllele(const(char)* r): Set REF allele only param r is \0-term Cstring TODO: UNTESTED
toString string toString(): Undocumented in source. Be warned that the author may not have intended to support it.

Properties

alleles string alleles [@property setter]: Set alleles; comma-separated list
alleles string[] alleles [@property setter]: Set alleles; array
allelesAsArray string[] allelesAsArray [@property getter]: All alleles getter (array)
altAllelesAsArray string[] altAllelesAsArray [@property getter]: Alternate alleles getter version 1: ["A", "ACTG", ...]
altAllelesAsString string altAllelesAsString [@property getter]: Alternate alleles getter version 2: "A,ACTG,..."
chrom string chrom [@property getter]: ///// FIXED FIELDS //////// Get chromosome (CHROM)
chrom const(char)[] chrom [@property setter]: Set chromosome (CHROM)
filter string filter [@property getter]: Get FILTER column (nothing in htslib sadly)
filter string filter [@property setter]: Set the FILTER column to f
filter string[] filter [@property setter]: Set the FILTER column to f0,f1,f2... TODO: determine definitiely whether "." is replaced with "PASS"
id string id [@property getter]: Get ID string
id const(char)[] id [@property setter]: Sets new ID string; comma-separated list allowed but no dup checking performed
pos int pos [@property getter]: Get position (POS)
pos int pos [@property setter]: Set position (POS)
qual float qual [@property getter]: Get variant quality (QUAL)
qual float qual [@property setter]: Set variant quality (QUAL)
refAllele string refAllele [@property getter]: Reference allele getter
refLen int refLen [@property getter]: REF allele length

Variables

line bcf1_t* line;: htslib structured record TODO: change to 'b' for better internal consistency? (vcf.h/c actually use line quite a bit in fn params)
vcfheader VCFHeader* vcfheader;: corresponding header (required);

VCFRecord

Constructors

Destructor

Members

Functions

Properties

Variables

Detailed Description

BCF UN ALL

BCF UN SHR

Meta

Source