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();

void chrom(const(char)[] c);

long pos();

void pos(long p);

string id();

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

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

long refLen();

string[] allelesAsArray();

string refAllele();

string[] altAllelesAsArray();

string altAllelesAsString();

void alleles(string a);

void alleles(string[] a);

void setRefAllele(const(char)* r);

void setAlleles(string _ref, string alt);

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

float qual();

void qual(float q);

string filter();

void removeAllFilters();

void filter(string f);

void filter(string[] fs);

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): Update FORMAT (sample info; column 9+) * * Templated on data type, calls one of bc_update_format_{int32,float,string,flag}
addFormat void addFormat(string tag, T data): Update FORMAT (sample info; column 9+) * * Templated on data type, calls one of bc_update_format_{int32,float,string,flag}
addID int addID(const(char)[] id): Append an ID (column 3) to the record. NOTE: htslib performs duplicate checking
addInfo void addInfo(string tag, T data)
void addInfo(string tag, T[] data): Update INFO (pan-sample info; column 8) * * Add a tag:value to the INFO column * NOTE: tag must already exist in the header * * Templated on data type, calls one of bcf_update_info_{int32,float,string,flag} * Both singletons and arrays are supported.
alleles void alleles(string a): Set alleles; comma-separated list
alleles void alleles(string[] a): Set alleles; array
allelesAsArray string[] allelesAsArray(): All alleles getter (array)
altAllelesAsArray string[] altAllelesAsArray(): Alternate alleles getter version 1: ["A", "ACTG", ...]
altAllelesAsString string altAllelesAsString(): Alternate alleles getter version 2: "A,ACTG,..."
chrom string chrom(): Get chromosome (CHROM)
chrom void chrom(const(char)[] c): Set chromosome (CHROM)
filter string filter(): Get FILTER column (nothing in htslib sadly)
filter void filter(string f): Set the FILTER column to f
filter void filter(string[] fs): Set the FILTER column to f0,f1,f2... TODO: determine definitiely whether "." is replaced with "PASS"
hasFilter bool hasFilter(string filter): Determine whether FILTER is present. log warning if filter does not exist. "PASS" and "." can be used interchangeably.
id string id(): Get ID string
id int id(const(char)[] id): Sets new ID string; comma-separated list allowed but no dup checking performed
pos long pos(): Get position (POS, column 2) * * NB: internally BCF is uzing 0 based coordinates; we only show +1 when printing a VCF line with toString (which calls vcf_format)
pos void pos(long p): Set position (POS, column 2)
qual float qual(): Get variant quality (QUAL, column 6)
qual void qual(float q): Set variant quality (QUAL, column 6)
refAllele string refAllele(): Reference allele getter
refLen long refLen(): REF allele length
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(): Return a string representation of the VCFRecord (i.e. as would appear in .vcf) As a bonus, there is a kstring_t memory leak

Variables

line bcf1_t* line;: Undocumented in source.
vcfheader VCFHeader* vcfheader;: Undocumented in source.

VCFRecord

Constructors

Destructor

Members

Functions

Variables

Detailed Description

BCF UN ALL

BCF UN SHR

Meta

Source