Implement support for indexing VCF files from the targeted genotyping

[Nicklas Nordborg]

See Reggie ticket #1323. The VCF files should be more or less compatible with the existing once from the regular variant calling. But there are some differences:

• Each VariantCall may have multiple VCF files from targeted genotyping. The should all be indexed in the same index.
• The AF (Allele frequency) and VD (Variant Depth) fields are not added by the HaplotypeCaller, but they can be calculated from the AD and DP fields.
• The VCF files also contain results for ​homozygous genotypes. They should be indexed since it may be useful to query everything, but some functions and information need to be changed since they are not all variants.

[Nicklas Nordborg]

In 6371:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Added an item list for handling targeted genotyping.

[Nicklas Nordborg]

In 6372:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Added an index for the targeted genotyping. It will not find any files to index yet.

[Nicklas Nordborg]

In 6373:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Added VcfFileLocator with two different implementations for finding the VCF files that should be indexed. This should work with the 3 different indexes (but support for more than one file has not yet been implemented).

[Nicklas Nordborg]

In 6374:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Added VcfFileLocator with two different implementations for finding the VCF files that should be indexed. This should work with the 3 different indexes (but support for more than one file has not yet been implemented).

[Nicklas Nordborg]

In 6375:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Indexing multiple VCF files should now work.

[Nicklas Nordborg]

In 6376:

References #1324: Implement support for indexing VCF files from the targeted genotyping

AF and VD are calculated from the AD annotation if needed.

[Nicklas Nordborg]

In 6377:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Indexing is now aware of different genotypes. A './.' call is not indexed since it means that there is no data. '0/0' is only indexed if the 'indexAllGenotypes' flag is enabled. Some counting function have been updated to only consider actual variants and there are new functions that also consider all genotypes.

[Nicklas Nordborg]

In 6379:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Minor changes in the hit details dialog since not all genotypes are variants.

[Nicklas Nordborg]

In 6380:

References #1324: Implement support for indexing VCF files from the targeted genotyping

When querying the targeted genotypes index we should only return results with a variant unless the query explicitely asks for other genotypes.

[Nicklas Nordborg]

In 6381:

References #1324: Implement support for indexing VCF files from the targeted genotyping

Ignore 'p.?' when indexing and displaying hits, since it is not very interesting.

[Nicklas Nordborg]

In 6395:

References #1324: Implement support for indexing VCF files from the targeted genotyping

If the genotype is './.' it is not a variant.