new enum htsjdk.variant.variantcontext.StructuralVariantType describing the SV types

[lindenb]

Description

As I'm playing with structural variation and the tool 'lumpy-sv', this PR introduces a new enum htsjdk.variant.variantcontext.StructuralVariantType describing the SV types defined in the VCFSpec 4.2:

##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
Value should be one of DEL, INS, DUP, INV, CNV, BND. 

• A constant SVTYPE was added in VCFConstants
• getStructuralVariantType() was added to VariantContext
• I've added a test and a test file src/test/resources/htsjdk/variant/structuralvariants.vcf that could become more complicated in the future (e.g: decoding the BND data).

Checklist

• Code compiles correctly
• New tests covering changes and new functionality
• All tests passing
• Extended the README / documentation, if necessary
• Is not backward compatible (breaks binary or source compatibility)

[coveralls]

Coverage increased (+0.03%) to 68.952% when pulling 01f913e on lindenb:svtype into c3d5a88 on samtools:master.

[droazen]

@cwhelan or @tedsharpe could one of you review this one?

[cwhelan]

This looks good to me; we've added similar stuff to GATKSVVCFHeaderLines but they probably belong in htsjdk instead.

While we're at it there are a number of SV-related spec-defined header lines like SVTYPE and SVLEN that could be added to htsjdk's VCFStandardHeaderLines class, but those might be able to go in under a separate PR.

[yfarjoun]

@cwhelan is this good to go? if so, could you bless it with a formal :+1: and also merge it?

[cwhelan]

I can give this a +1 but I can't merge. @droazen?

[d-cameron]

I for one, would love for all of the spec-defined SV headers to be included in htsjdk (ie, everything in https://github.com/PapenfussLab/gridss/blob/master/src/main/java/au/edu/wehi/idsv/vcf/VcfSvConstants.java and https://github.com/PapenfussLab/gridss/blob/master/src/main/java/au/edu/wehi/idsv/vcf/VcfStructuralVariantHeaderLines.java).

Be aware that some SV callers write SV types that are not in that enumeration (earlier versions of the the spec were less restrictive than v4.3). Notable callers include DELLY writing TRA, TIGRA writing CTX, and Pindel writing RPL.