Nils Homer

Add metric builder and sorter

2

Added a new class `MetricSorter` that's useful when we want to sort metrics but cannot hold them all in memory. Leverages `Sorter`.

Feature to have ZipperBams output to SAM format

2

So the output of ZipperBams can be fed directly into samblaster without a `samtools view -h`.

Add scala implementations for some SamRecord methods

4

* refPosAtReadPos * readPosAtRefPos

Needs tests

In a lot of places we check if the input SAM header is queryname or query group sorted. We should have a single function in `Bams` to do this. I...

The `--by-sample` argument will now group input reads by their sample name specified in their corresponding read group. In this case, reads without a read group are ignored, and read...

Adding a tool to validate VCFs

1

There are other tools out there. The motivation for this tool are: 1. Validates the VCF header, including against spec-reserved header values (id, type, and count) 2. Validates types and...