bug 20755
   First, change the option name from -mapSubreadsOfZmwTogether to -concordant.

   Second, since the longest subread is usually not the best template subread,
   now with this option blasr aligns subreads of a zmw to where the 
   longest *internal* subread (which has adpters at both ends) has aligned to.

   Third, flanks the template alignment target (i.e. where the longest internal 
   subread has aligned to) by a certain number of bases for other subreads to
   map to. The default value is 40 for now. The flank size can be specified by 
   a hidden option -flankSize.

   Fourth, blasr now checks whether names of references (truncated by the very
   first space) are unique. If not, exit with an error.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124878]
   bug 23171
   blasr now accepts *.ccs.h5 file (or fofn) as its input and maps ccs 
   to reference. The results of:
     blasr *.ccs.h5 ref.fasta 
   should be exactly the same as:
     blasr *.bas.h5 ref.fasta -useccsdenovo
   , where the bas.h5 and ccs.h5 have exactly the same data group: 
     /PulseData/ConsensusBaseCalls.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124937]
   bug 18909 
   Update Makefile. Add -ldl, move -lpthread to the end of rules to avoid
   compilation errors in some environments.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124950]
   bug 18909 
   Add git hub repo script tag for google analytics. 

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124972]
   bug 18909
   Fix a bug when loading pulse info to denovo ccs alignments.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125043]
   bug 18909
   Rename LoadPulses2.cpp as LoadPulses.cpp	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125049]
   bug 22808
   Change output cmp.h5 files read type to 'CCS' instead of 'Standard' when 
   --useccs=useccsdenovo is specified.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125052]