VcfReader.php
Reads a VCF file into VcfVariant instances Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 6 October 2026
Table of Contents
Classes
- VcfReader
- A standalone, persistence-independent text reader, the same spirit as GffFeatureReader and BedFeatureReader : "##" meta-information lines and the single "#CHROM..." column-header line are skipped, data lines are tab-separated, a malformed one is reported as a warning and skipped rather than crashing the whole read. Only the 8 mandatory fixed columns (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO) are read ; FORMAT and per-sample genotype columns, when present, are ignored - modeling genotypes/samples is a substantially bigger undertaking than a tabular reader, out of scope here the same way BED12's block columns are out of scope for BedFeatureReader.