Fix bug 25675

BasH5Reader wasn't honoring the "chemistry override" semantic allowed
by the spec.  This patch brings BasH5Reader in line with the spec.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 139586]
Restore semantic of chemistryBarcodeTriple

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 139597]
Bug 25598

Update chemistry mapping.xml files to reflect 2.3 basecaller version and the new barcodes fot P6-C4

The file in SMRTpipe should not be used anymore, but I am deferring the removal of that til 2.4.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 139610]
Version 0.9.0 for smrtanalysis-2.3

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 139761]
Prospective API for accessing (adapter, insert) regions and corresponding data.

New method names include "NoQC" and have warnings in the document, so
it should be clear that these methods are for expert use only.

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 140322]
[bug 25846] Commiting new BarcodeH5Reader/Fofn functionality and test

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 140981]
Make file non-executable so tests get picked up by nose

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 140984]
Bug 25852. Mysteriously fix Quiver's HDF5 infinite loop problem. At least sometimes.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141230]
[bug 25894] Cleaning up end-of-line whitespace from various files

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141399]
   Bug 25779. Add test BAM file to pbcore.data that conforms to the PacBio spec.

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141400]
           [bug 25890] Adding chemistry caching to BasH5IO and associated tests

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141402]
[bug 25897] Adding reverse complementing to pbcore and associated unit tests

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141454]
       [bug 25895] Adding "Id" and "Metadata" support to sequence records and associated unit tests

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141455]
[bug 25895] Converting default value of the Metadata fields to None

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141469]
[bug 25895] Fixing test code to better follow coding guidelines for line-continuation

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141507]
[bug 25897] Added error-checking to reverseComplement and associated tests

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141516]
[bug 25895] Changing the import of utils to better follow coding guidelines

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141518]
[bug 25897] Performing evil, pre-mature optimization of non-core code for reverse complementation

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141520]
[bug 25897] Changing util import to no longer break in downstream cram/doc tests

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141533]
Fix test, and remove executable bit so nose will find it

[Tracking bug 25700]

[git-p4: depot-paths = "//depot/software/smrtanalysis/bioinformatics/lib/python/pbcore/": change = 141543]