One case that fails to produce correct output is when merging headers where one header has a dictionary that is a subset of the other. Given two headers, one header with contigs "1" through "22" and one with contigs "20" and "21":
getContigLines returns the lines ordered "20", "21", "1", "2", "3", "4", ..., "19", "22" (all lines are included, but are out of order)
getSequenceDictionary has the lines ordered "20", "21", "3", "4", ..., "19", "22" (contigs "1" and "2" are missing entirely, remaining order is incorrect)
getemtaDataInSortedOrder - (which is used by VCFWriter to serialize the VCFHeader on write), same result as getSequenceDictionary, (contigs "1" and "2" are missing entirely, remaining order is incorrect)
Though I suspect these results depend on the order in which the headers are merged.
One case that fails to produce correct output is when merging headers where one header has a dictionary that is a subset of the other. Given two headers, one header with contigs "1" through "22" and one with contigs "20" and "21":
Though I suspect these results depend on the order in which the headers are merged.
See https://github.com/samtools/htsjdk/issues/1573, which is the root cause of much of this.