Parallel bgzip with cram support #21
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…allel-bgzip-cram Conflicts: Makefile bam/Makefile.depends bam/SamRecord.cpp general/BgzfFileType.h general/PhoneHome.cpp
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It will likely take a while before someone can review this. |
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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! |
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@Santy-8128 @jonathonl Can you take a look at this pull request, and commit if passes muster. |
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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-supportbranch. I pulled that branch into mine, which solved the samtools issue. However, that also had the effect of mergingmasterandcram-supportin my topic branch.Where
masterandcram-supportdiffer, 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 ingeneral/test.Let me know if there are any changes to the PR needed to aid acceptance.