Switched order of Number and Type keys in VCF END2 meta info line causes problems in htsjdk

[cwhelan]

Module0506's postCPX_cleanup.py writes the END2 meta info line as:

##INFO=<ID=END2,Type=Integer,Number=1,Description="Position of breakpoint on CHR2">

The switch from the usual ordering of Number,Type causes htsjdk to throw an error when trying to parse the file:

htsjdk.tribble.TribbleException$InvalidHeader: Your input file has a malformed header: Tag Type in wrong order (was #2, expected #3) in line <ID=END2,Type=Integer,Number=1,Description="Position of breakpoint on CHR2">
        at htsjdk.variant.vcf.VCF4Parser.parseLine(VCFHeaderLineTranslator.java:172)
        at htsjdk.variant.vcf.VCFHeaderLineTranslator.parseLine(VCFHeaderLineTranslator.java:58)
        at htsjdk.variant.vcf.VCFCompoundHeaderLine.<init>(VCFCompoundHeaderLine.java:215)
        at htsjdk.variant.vcf.VCFInfoHeaderLine.<init>(VCFInfoHeaderLine.java:56)
        at htsjdk.variant.vcf.AbstractVCFCodec.parseHeaderFromLines(AbstractVCFCodec.java:192)
        at htsjdk.variant.vcf.VCFCodec.readActualHeader(VCFCodec.java:111)
        at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:79)
        at htsjdk.tribble.AsciiFeatureCodec.readHeader(AsciiFeatureCodec.java:37)
        at htsjdk.tribble.TribbleIndexedFeatureReader.readHeader(TribbleIndexedFeatureReader.java:261)
        ... 16 more

[nh13]

@cwhelan just hit this issue, I am not 100% certain if this is a bug in htsjdk or a bug here.

See: samtools/hts-specs#642

[cwhelan]

Yes, we changed the order of the tags a while back on our end but it looks like you're using a VCF generated before that.

Personally I don't think the order of the keys should matter in a list with key-value pairs, and I think I asked about changing this in htsjdk briefly when it cropped up, but the spec was just ambiguous enough, and htsjdk had old explicit logic and test cases trying to enforce this rule, that there didn't seem to be enough clarity to push through a change to htsjdk. Happy to put in a plug on the hts-spec issue in favor of explicitly dropping the order restriction.