LoadPulse prints a correct warning message when no alignments between
   an input bas.h5 file and reference are found in the input cmp.h5 file.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125846]
   Correct the bug that coordinates of some alignment targets may off
   by flankSize. 
   Reset default minMatch to 12.
   bug 23702

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125859]
   Add a test case for blasr -concordant.
   bug 23702	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125863]
   Add -header	for m5 (machine-parsable format for compareSequences.py) format.
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 125880]
samtoh5 now accepts reads in two types of format:
   "movie/zmw/start_end" and "movie/zmw/start1_end1/start2_end2"
   bug 23340

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126156]
   pls2fasta prints an error message when input *.bas/pls/ccs.h5
   files corrupted.
   bug 23176

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126180]
   Update cram tests for loadPulses and samtom4.	
   bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126181]
   Fix a bug which makes loadPulses load incorrect pulse data when 
   input file is *.pls.h5 and -byread is specified simultaneously.
   bug 18909	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126307]
   The mapping between base types (i.e., ATGC) to channels (i.e., column orders
   in /PulsesCalls/MeanSignal) is obtained from /ScanData/DyeSet/BaseMap, 
   instead of being fixed (i.e., G=1, T=0, A=2, C=3).
   bug 23782

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126356]
   Fixed an invalid assumption which assumes that PulseCalls/ZMW/HoleNumber is 
   identical to BaseCalls/ZMW/HoleNumber.
   Fixed a bug (introduced by change 126307) which uses holeNumber as index 
   when -byread is specified.
   bug 23782

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126407]
Add argument sanity checks for samtoh5.
Update version numbers for samtoh5, samtom4, loadPulses, pls2fasta and blasr.
bug 18909

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126424]
   Compute MapQV for ccs reads instead of using hard-coded value (50).	
   bug 23729

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 126469]