Bug 23016

Fixed relative path for swigwin in windows build.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 140960]
Allow cross platform compilation for consensuscore (Bug 25700)

The following changes were made to allow compilation on windows: 
* Avoid naming conflict in DELETE definition from windowsnt.h
* Avoid naming conflict in max function in windows.h
* Upgrade to boost 1.55
* Comment out unused function that throws errors
* Change path to new swig location.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 140985]
Missed file in windows compatability commit (Bug 25700) 

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 140986]
Fix a goof

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 140987]
Add an option -minRawSubreadScore to blasr, which filters raw subread whose
quality score in region table is less than a threshold. 
bug 25766	

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141053]
Update -minSubreadScore and add a cram test. 
bug 25766

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141081]
   Bug 25807. Fix off by one that made SubstitutionTag get printed twice.	

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141198]
Add -concordantTemplate 'mediansubread', which uses the median length 
full-pass subread of a zmw as template for concordant mapping. 
Change default value of concordantTemplate from 'typicalsubread' to
'mediansubread'.
Add more unittest tests for alignment/utils/RegionUtils.
Update blasr cram tests.
bug 25860	

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141378]
Move a bax.h5 for testing FragmentCCSIterator to /mnt/secondary-siv/testdata/.
bug 25860

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141384]
Blasr exits with an error message when mmap fails.
bug 25661	

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/cpp/": change = 141406]