Integrated DPC native and triplet pipeline density estimation functions

[sdentro]

This is phase 2 of the integration of the triplet pipeline into the main DPC package. This now includes the density estimation code that will work in the triplet pipeline and is setup to seamlessly integrate into the standard code without any changes to pipelines to be done. Therefore, to test this new code, it should just run on any sample/case where the triplet pipeline is not required.

For the triplet pipeline, two output files are now slightly different. It either required changing the DPC package code, or a change to the triplet pipeline. I've opted for the latter. This will require a small change to the code that combines the triplet density output. This is underway and will come in phase 3. But for the sake of completeness, these files are different from the current separate triplet pipeline:

• [samplename]_[triplet id]_DP_and_cluster_info_0.01.txt -> no longer has chr/pos columns
• [samplename]_[triplet id]_optimaInfo_0.01.txt -> now has cluster.no column

The last paragraph was more for information only. The changes in these commits should integrate without any adaptation of the regular pipeline required and I'm very happy to take feedback where it doesn't!

[sdentro]

The second and third commits to this contains what I'm referring to as "phase 3": The code that was previously not yet included in the package.

The final phase 4 will add docs and instructions on how to run the triplet pipeline via the package. Then this would be ready for release

[sdentro]

The last commit contains a fully working triplet pipeline with it's own example scripts and data (and a rebase to incorporate changes in master branch since starting this work). This means that "phase 4" is now fully complete and this work is done.

It is important to mention that I no longer have access to real world data. The triplet pipeline behaves exactly as it does on real data in my experience, but some more testing would be good before fully accepting these changes into the main package.