VCFHeader has no guard against multiple contig header lines with the same contig index. Also VCFContigHeaderLine has a compareTo implementation that ignores everything except for contigIndex, which makes it inconsistent with both equals and hashCode.
Set implementations that use a comparator, such as TreeSet, treat two VCFContigHeaderLine as equal if they have the same contig index, which is different than other non-comparator based sets. This results in various inconsistencies when two lines with the same index are included in a header (which can happen when merging headers, or manually creating headers):
VCFHeader.getContigLines returns all lines, even ones with a duplicate index, sorted in input order (does not respect contig index order)
VCFHeader.getSequenceDictionary uses getContigLines, so it also includes all lines in input order (does not respect contig index order)
VCFHeader.getMetaDataInSortedOrder() (this is what is used by vcfWriter to serialize a header) respects contig index order because it uses an intermediate TreeSet, and also returns only one from the duplicate set
VCFHeader has no guard against multiple contig header lines with the same contig index. Also VCFContigHeaderLine has a
compareToimplementation that ignores everything except forcontigIndex, which makes it inconsistent with bothequalsandhashCode.Set implementations that use a comparator, such as TreeSet, treat two VCFContigHeaderLine as equal if they have the same contig index, which is different than other non-comparator based sets. This results in various inconsistencies when two lines with the same index are included in a header (which can happen when merging headers, or manually creating headers):