Fixed some build issues, mostly with typos and file paths

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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Fixed some build issues, mostly with typos and file paths #4

Closed SHuang-Broad closed 8 years ago

SHuang-Broad commented 8 years ago

Added Concurrency module copied directly from SGA's master branch.

Modified configure.ac and various Makefile.am files in SGA subdirectory to correct for file dependency path.

SHuang-Broad commented 8 years ago

Forgot to mention: prior to ./configure, ./autogen.sh is necessary.

walaj commented 8 years ago

Awesome, thanks for helping fix the build! I put all of the changes in except for adding Concurrency. My thought was that I want to keep the API components on one thread, and leave multi-threading implementation up to the user. I suppose the SGA could be baked into the API at some point if people wanted to call heavy-duty assemblies, but I haven't pursued this yet.

SHuang-Broad commented 8 years ago

Glad I can help.

The reason why I brought Concurrency in is that some functions in SGA/Algorithm, SGA/SGA and SGA/SuffixTools seem to depend on SequenceProcessFramework.h defined in Concurrency. So when I tried to build, the compiler issued errors without bringing in Concurrency.

Anyway, definitely fine and quite good to plan ahead for consistent API.