Aaron Lun

Add a Bunis HSPC data getter

4

@dtm2451 the time has cometh. Should be as simple as copying one of the other getters to `BunisHSPCData.R`, renaming the function and changing the path to `bunis-hspc`. - Make sure...

When we need to figure out how to smash multiple parts together, allow users to choose between: - Taking the intersection of genes across all parts. - Taking the union...

Currently the Ensembl version is hard-coded at my choice of AH number, but there's no reason to limit users to that. The idea here is to support `ensembl = "99"`...

Data from Yao

2

@ahy1221: I'll apologize for not answering your email directly; my old CRUK account forwards my mail but _does not forward the sender address_, leaving me unable to respond directly to...

This should also take care of setting `correct.all=TRUE`.

Convert `Number=A` to `Number=1` when creating an `ExpandedVCF`

5

It seems reasonable that per-allele `##INFO` fields should be converted from `Number=A` to `Number=1` when `expand()` is called, given that the 1:many relationship between rows and allelic values is now...

`readVcf` doesn't handle quoted `=` in `hapmap_exome_chr22.vcf.gz` correctly

8

The header line for `GATKCommandLine` causes problems: ``` ##GATKCommandLine= ``` Calling `readVcf` gives me: ```r fl

Faithfully recapitulate metadata via a round-trip through `writeVcf` + `readVcf`.

4

`writeVcf` performs some unnecessary work that interferes with a perfect roundtrip of a `VCF` to a file and back. At the very least, these discrepancies interfere with my unit tests...

Making the CompressedList more widely usable

4

I've been playing around with the `CompressedList` subclasses for representing some complex data types and I've really come to like it. I've been thinking of ways to make it more...