libStatGen Parallel bgzip with cram support

This PR request is related to #20. This branch was started off of the master branch, with the goal of adding support for parallel bgzip to InputFile. I was successful in my endeavor; one can now open a bgziped file in parallel by adding @<numThreads> to the mode specification.

During development, it was discovered that supporting the build process with samtools as a dependency was painful. As suggested by @jonathonl, I looked into the cram-support branch. I pulled that branch into mine, which solved the samtools issue. However, that also had the effect of merging master and cram-support in my topic branch.

Where master and cram-support differ, I do not know which code base is preferable, e.g. Chromosome.cpp. I also do not have a way to perform regression tests for correctness, other than having run the binaries in general/test.

Let me know if there are any changes to the PR needed to aid acceptance.

Oct 10 '18 19:10 daheise

It will likely take a while before someone can review this.

Oct 12 '18 18:10 jonathonl

Since it's been over a month I wanted to check in and see if there is any update on how long it might be before a review is able to be conducted. Thanks!

Dec 03 '18 17:12 daheise

@Santy-8128 @jonathonl Can you take a look at this pull request, and commit if passes muster.

Mar 21 '19 15:03 avsmith