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walaj / SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data
http://bioinformatics.oxfordjournals.org/content/early/2016/12/21/bioinformatics.btw741.full.pdf+html
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Use system htslib; a couple minor tweaks #64

Open julianhess opened 3 years ago

julianhess commented 3 years ago

The htslib submodule was getting stale; I think it's better if we use whatever system htslib is already included.

Also implemented a more efficient way of getting the number of softclipped bases, and provided a function for getting the current region index.

julianhess commented 3 years ago

BTW, it looks like we have to update the test suite VM to include an installation of htslib.

walaj commented 3 years ago

I think this makes sense, thanks for the updates. I'd like to see it pass the test suite first. Can you add the following to travis-before-install.sh? That should work. I made a branch jhess with this, but can't figure out how to get Travis CI to build this branch.

    ## install htslib
    mkdir htslib
    wget --no-verbose --output-document=- https://github.com/samtools/htslib/releases/download/1.12/htslib-1.12.tar.bz2 | tar xfj - --strip-components=1 -C htslib
    cd htslib && ./configure
    sudo make
    sudo make install