Update blasr affine align.
   Update HDFBaseWriter. 
   Update ComputeAlignmentStates and fix a bug in computing edit distance.
   Clean up code.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128509]
   Update cram tests and unit tests. 
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128510]
   Update simulator alchemy and StoreQualityByContextFromCmpH5.
   bug 24012

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128513]
   Update unit test.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128514]
   Update SDPMatcher. 
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128522]
bug 23997 updating makefiles to turn gtest xml output on

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128733]
bug 23997 coupleof makefile updates anda typo

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128761]
   Remove -g from make rule for compiling loadPulses.
   bug 18909	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128771]
   pls2fasta no longer requires pls/bas.h5 file to be placed in the same
   order as their corresponding region tables. However, this additional
   sanity check leads to slightly increased run time when there are many 
   bas.h5 files.
   bug 24229	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128927]
   bug 21591
getting pelusa to compile

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129130]
bug 21591
   small cram test for pelusa

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129131]
   bug 21591
medium test

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129132]
   Fix a memory leak.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129158]
bug 21591
   added a targetFeatureStride to pelusa. 

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129212]
   Fix a memory leak.
   Bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129222]
bug 21591
   unique pelusa kmers

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129252]
bug 18462, bug 24066, bug 18909
       - Bump hdf5 and h5py version
       - Change HDFAttributable.h to suppport hdf5 1.8.12. (@129255 by yli@yliWorkspace on 2013/11/20 10:29:23)

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129340]
bug 18909 - temporarily reverting hdf5

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129344]
   Add support for compiling against both hdf 1.8.12 and hdf 1.8.4
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129383]
  Add support for both hdf 1.8.4 and hdf 1.8.12
  bug 18909	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 129385]