Adding matplotlib dependency for pbh5tools first and we talk about
getting rid of this dependency later. - bug 21713

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119647]
Stop using the defunct pbcore.io.cmph5 APIs.

[Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119674]
Added an examples.t which produces an examples.html using cram+pandoc. Added general documentation to the Metrics and Statistics.


bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119765]
Fixed absolute path issue.

bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119772]
Fixed sorting to be stable across split/merge/sort invocations.

The primary issue was that refID is a mapping to a refInfoID, the refInfoID should be stable across different manipulations of the file (Although that is not in the spec)

bug 22557

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119827]
failed to checkout these tests.

bug 22557

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119828]
Fixed to return return codes that are correct.

bug 22579

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 119891]
       Fix the tools (CmpH5Reader API change)

       [Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120021]
       CmpH5Reader API change (movieTable -> movieInfoTable)

       [Tracking bug 21562]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120073]
Fixed behaviour when no arguments are passed to 'stats'

bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120277]
Big speedup in some of the core metrics. Removed outdated index.rst and replaced with README.rst. 

bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120440]
Fix for final API changes to pbcore. Additionally, change to produce data in a more natural order.

bug 21763

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120464]
Bug 22350 - Shebang in this file is not correct, move the '#!' to the first line
to work with minimal installed ubuntu 12.04
prop:S2.0

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbh5tools/": change = 120777]