bug 21044

Added a new merge tool to better support multi-part file processing. 

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 118963]
bug 21044

made the new merge code the default.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 118972]
bug 21044

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119002]
Bug 21044. Fix broken import in cmph5tools.py

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119046]
bug 21044

Cleaned up some of the interfaces fixed some edge cases.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119053]
bug 21044

missed this one.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119081]
bug 21044

Fixed improper writing of path dataset. Also, fixed reset of MOLECULE and ALIGNMENT IDs.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119094]
bug 22456

Added tests for merge, select, equal and sort. Need to expand the test file availability to really make these tests tough.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119140]
bug 21044

fixed mistaken identity.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119151]
bug 22455

added a sanity test to pbbarcode which runs through each of the subcommands. It does no checking of correctness though.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119152]
bug 21044

Fixed out-of-spec hdf5 data types.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119189]
bug 22485

Sort now produces ascending read group numbers rather than randomly chosen ones.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119256]
bug 21763 	

Fixed re-raising of exception. Interestingly, re-raising an exception in python has a goofy syntax. Also, first cut of the stats module.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119301]
bug 21763

Added the Metrics module, added support for where and groupBy expressions in the select utility. Added some tests, need to get larger files. 

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119316]
bug 21763

More fleshed out CmpH5Select and Stats. No more split, hence the break in enzymologyAnalysis.R

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119328]
bug 21763

added an example.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119348]
bug 21763

A number of fixes / additions for supporting bb.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119390]