Service
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.
- VcfVariantRecordMapper
- Class VcfVariantRecordMapper
- VcfWriter
- 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.