Documentation

VcfWriter
in package
implements VcfWriterInterface

VCF 4.3 : "##fileformat=VCFv4.3", the extra meta lines, "#CHROM POS ID REF ALT QUAL FILTER INFO", then a tab-separated line per variant. A missing value (no ID, no ALT, no QUAL, no FILTER, no INFO) is ".". The ALT alleles are joined by commas, the INFO entries by semicolons, a flag written by its key alone, and an INFO value has its ";", "=", ":", "%" and line or tab characters percent-encoded (the reader decodes the same set) - its commas are not, since they separate the items of a list.

Positions are written as they are held, 1-based. VcfReader reads back what this writes. Class VcfWriter

Tags
author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

VcfWriterInterface
Interface VcfWriterInterface - the counterpart of VcfReaderInterface : writes VcfVariant instances as a VCF file with its eight fixed columns (no FORMAT, no sample genotype).

Constants

COLUMNS  : mixed = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
FILE_FORMAT  : mixed = "##fileformat=VCFv4.3"
INFO_ENCODING  : array<string|int, string> = ["%" => "%25", ":" => "%3A", ";" => "%3B", "="...
MISSING  : mixed = "."

Methods

write()  : string
assertOneLine()  : void
encodeInfoValue()  : string
A "%2C" is left as it is : VcfReader keeps an encoded comma encoded, so a value read from a file holds "%2C" for it, and encoding its "%" again would write "%252C", the text "%2C" instead of a comma.
writeInfo()  : string
writeVariant()  : string

Constants

COLUMNS

private mixed COLUMNS = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"

FILE_FORMAT

private mixed FILE_FORMAT = "##fileformat=VCFv4.3"

INFO_ENCODING

private array<string|int, string> INFO_ENCODING = ["%" => "%25", ":" => "%3A", ";" => "%3B", "=" => "%3D", "\r" => "%0D", "\n" => "%0A", "\t" => "%09"]

What strtr() replaces in one pass, so a code it adds is never encoded again

Methods

write()

public write(array<string|int, VcfVariant> $aVariants[, array<string|int, string> $aMetaLines = [] ]) : string
Parameters
$aVariants : array<string|int, VcfVariant>
$aMetaLines : array<string|int, string> = []
Return values
string

assertOneLine()

private assertOneLine(string $sLine, string $sWhat) : void
Parameters
$sLine : string
$sWhat : string
Tags
throws
InvalidArgumentException

encodeInfoValue()

A "%2C" is left as it is : VcfReader keeps an encoded comma encoded, so a value read from a file holds "%2C" for it, and encoding its "%" again would write "%252C", the text "%2C" instead of a comma.

private encodeInfoValue(string $sValue) : string
Parameters
$sValue : string
Return values
string

writeInfo()

private writeInfo(array<string, string|bool> $aInfo) : string
Parameters
$aInfo : array<string, string|bool>
Return values
string

writeVariant()

private writeVariant(VcfVariant $oVariant) : string
Parameters
$oVariant : VcfVariant
Return values
string —

The variant's tab-separated line, without its newline

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