Fix mapQV: when bestn > 1 and a potential alignment candidate is  
a subsequence of another, correct mapQV will be computed. 
Usually the second best alignment is a subsequence of the best hit (e.g., a
copy of a mobile element spaning over the genome). 
With this fix, a very low mapQV will be assigned to the second best hit.
bug 24363

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133414]
blasr, pls2fasta, loadPulses support the new bas.h5 files which contain no
/PulseData data, but have /MultiPart/Parts.
bug 24173

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133643]
Fix Makefile for bsdb: hdf5 lib is required to compile bsdb
bug 24173 

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133657]
Fix samFilter -hitPolicy=randombest or allbest
bug 25062	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133713]
Compute correct mapQV when -affineAlign is specified or when input 
reads are in fasta format.
bug 24363

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133977]
Migrate blasr unit test datasets to /mnt/secondary-siv/testdata
Update missing pls.h5 files and Makefile
bug 24733	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133988]
Update blasr/samFilter/loadPulses's cram tests to use datasets 
in /mnt/secondary-siv/testdata
bug 24733

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 133996]
Update SDPAlign.
   Update cram tests accordingly.
bug 24413	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 134507]
Use GraphPaper to speed up SDPAlign.
bug 24413	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 134961]
Add hitPolicy left most to samFilter.
bug 25215	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 134995]
Update function AlignmentsOverlap to check whether queries of two 
alignments overlap or not.
bug 23801

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135057]
Update function AlignIntervals. Print more info when verbosity > 0
bug 24437	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135064]
Add minAlignLength to MappingParameters.h.
bug 24437	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135072]
Enable a new clip mode 'subread' for SAM output, which soft clips seqs within 
coordinates of subreads instead of unrolled reads.

Enable a new option: -printSAMQV. When printSAMQV is specified, blasr prints
additional quality values including InsertionQV, DeletionQV, SubstitutionQV,
MergeQV, DeletionTag, MergeTag, to SAM output.

bug 24361

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135239]
Use MAX_BAND_SIZE to contain search space of banded alignment.
bug 24437

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135254]
Update FindMaxInterval to improve speed. As a result, alignments produced 
by blasr will change accordingly (based on an ecoli test case, sensitivity 
is slightly reduced by < ~0.1%)

Update cram tests accordingly

bug 24437	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135288]
Update SparseDynamicProgramming (e.g., update SDPLongestCommonSubsequence,
sort SDP fragments both horizontally and vertically, and only search space
above a certain threshold to gain speed up).

Update cram tests.

bug 24437	

[git-p4: depot-paths = "//depot/software/assembly/cpp/": change = 135306]