[BioLib-dev] Merging libsequence into main

[Pjotr Prins]

Hi Xin,

I have started merging your tree into the release candidate. I have
pulled from your master_conflict branch (a bit odd name ;) and
adjusted one major thing. Since libsequence needs the Boost++
libraries I have added those as a git submodule. After pulling from my
libsequence branch at git at github.com:pjotrp/biolib.git (using git
remote) you should see commit
8aa0e29ced45f24463f78804b718119c4412005a. Next update the submodules.
Like this:

  git submodule -i update

it will pull boost into root contrib directory ./contrib/boost/...

I had to adjust some of your make files to match the new layout. So 
when you do:

  cd src/clibs/libsequence-1.6.6/src
  rm CMakeCache.txt
  cmake .
  make

it should build the library in ../build fine.

Next go to your Python mappings

  cd src/mappings/swig/python/libsequence
  rm CMakeCache.txt
  cmake .
  make

and I get the error:

/home/wrk/izip/git/opensource/biolib-libsequence/src/mappings/swig/python/libsequence/../../../../../contrib/libsequence-1.6.6/Sequence/AlignStream.hpp:65:
Error: Syntax error in input(3).

After pulling my tree, can you have a look into this? Do you see the
same?

Pj.