Initial import of //depot/software/bioinformatics/tools/pbbarcode/ from the state at revision #head

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122556]
Accomodate slight pbcore ToolRunner API changes

[Tracking bug 22690]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122558]
Added a number of of scoring features -- still somwhat in validating. Also, some API updates for an untested branch of code.

bug 23097
bug 23059

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122663]
actually fixed this bug.

bug 23097

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122664]
Implemented better paired scoring mode. In addition, added much more information to the barcode.h5 files.

bug 22894

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122690]
bug 22894 - fix the shebang '#!' which should at the first line.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122839]
Added a MPBarcodeH5Reader class to proxy in case of multi part. Determination of whether a file is multi part or not is a little suspect, but should be okay.

bug 23136

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122946]
Small fix to make sure that it works with both absolute and relative paths in the fofn (I wonder if there is anything spec'd around that)

bug 23136

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 122947]
addded pbbarcode.py consensus to do a barcode+hgap+quiver consensus. This is currently achieving pretty good performance across phi29 datasets and possibly the fluidigm dataset, although there, I'm not sure I know the ground truth. 

bug 23241

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123298]
bug 22329 housekeeping integration of barcode stuff to mainline, (actually keeping jim's mainline fixes) 

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123329]
bug 22329
Rollback //depot/software/bioinformatics/tools/pbbarcode/src/python/pbtools/pbbarcode/BarcodeLabeler.py to revision 11

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123331]
bug 22329
Rollback //depot/software/bioinformatics/tools/pbbarcode/src/python/pbbarcode.py to revision 29

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123333]
Added some additional facilities for subsampling.

bug 23241

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123453]
Added another test, cleaned up some code, but more refactoring is needed.

bug 23059

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 123841]
To bug fixes for emission of FASTA/Q files that were discovered in a 2.0.1 development. Not integrated because of too many other code incongruencies.

bug 22921

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 124790]
bug 22891 major secondary documentation refactoring

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 125251]
Large number of refactoring changes to support CCS move, scoreFirst, filtering and other features.

This change also breaks the external API to conform with our coding standards and pbcore. Mainly, ZMW goes to Zmw. This will need to be changed in the modules.

bug 23282
bug 23172

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 125744]
Checkin for reads of insert. Now, if the fofn is a ccs fofn CCS reads are emitted if it is a bas.fofn then subreads are emitted. If the file has both the --subreads flag still works - allowing one to force the issue.

bug 23172

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 125750]
Updated the functional specification so that it wasn't completely wrong. Still needs some tuning.

bug 23172

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 125751]
Added an option to emit the FASTA/Q for unlabeled ZMWs. 

bug 23124

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbbarcode/": change = 125769]