Minor changes to "make clean".
   bug 19809	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128116]
   Make samtoh5 mimic the behaviour of compareSequences.py and remove
   reference groups which contain no alignments.
   Update cram tests.
   bug 23975

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128136]
   change type of minAccuracy and minPctSimilarity of samFilter from int to 
   float and add sanity check.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128274]
   Add an experimental option -titleTable to samFilter. This option can be
   useful for metagenomics, in which case there are hundreds of sequences
   in the target, of which many titles are long and may contain white spaces.
   One may call blasr with "-titleTable fileName" to represent all target 
   sequences in the output by their indices in the title table, then call
   samFilter with "-titleTable fileName" to filter the generated SAM file.
   Update unit tests.
   Bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128325]
   samtoh5 accepts "movie/holenumber" as valid pacbio read name.
   bug 18909	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 128339]