bug 22808
Add a new executable samFilter to filter SAM alignments based on
   minimum accuracy, minimum percentage similarity, minimum alignment length 
   and multiple-hit policy.
   Also fix a Makefile bug that breaks secondary-mainline-centos63 build

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 122699]
bug 22808
   Add support for bowtie. One can use "--algorithm=bowtie" if bowtie2 
   has been installed to the system PATH. 
   Add unit tests for BowtieService.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 122744]
trying to fix CI build, but it only fail at the second make. - bug 22350

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 122817]
bug 22350 - attempt to fix CI breakage again.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 122836]
   bug 18909
   update samtoh5 -smrtTitle description.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123205]
bug 22808
   Add an option -holeNumbers which specifieds a list of hole number ranges
   to output alignment hits.
   Update cram test for samFilter.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123260]
bug 22808
   Add a new option -holeNumbers to blasr. With this option, blasr only 
   aligns reads of which hole numbers are within the specified ranges.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123265]
   bug 23264
   blasr sam output nm tag now represents the edit distance.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123413]
   bug 23203
   loadPulses loads complete /AlnInfo/NumPasses for a ccs cmp.h5 file 
   which has been generated from multiple movies.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123440]
   bug 23267
   samFilter now groups alignments by target (reference) names and then 
   read groups (e.g. movie names).

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123448]
bug 23264
   Add a cram test for nm tag (edit distance) of blasr sam output.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123505]
bug 18909
   Update blasr -holeNumbers option description.
   UPdate comments in loadPulses.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123506]
bug 23277
   Fix bugs under depot/software/assembly/cpp detected by coverity.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123507]
   bug 23277
   fix bugs detected by coverity.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123510]
   bugs 23277  
   fix bugs detected by coverity.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123847]
bug 22808
   Improve samFilter speed.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 123888]
   bug 22935
   First, fix a bug that makes blasr generate incorrect alignment coordinates
   using -useccsall and -useccs options.
   Second, fix a bug that aligns subreads of a ccs read to different 
   genomic locations. Now, with '-bestn N -useccs' (or '-bestn N -useccsall'), 
   all subreads of a ccs will align to exactly N best genomic locations where
   the ccs aligns to. 

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124163]
   bug 22935
   Re-factor code aligning subreads of a zmw to where the ccs aligned to.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124193]
   bug 18909
   Format Blasr.cpp to improve readability.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124201]
   bug 23431
   Fix a bug that assigns incorrect pass directions to subread intervals.
   Also make sure that blasr produces determined results when -useccsall
   and -nproc N (where N > 1) are used.

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 124274]