Get rid of extraneous src/ directory

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127225]
Move BasH5IO module to the shameful "deprecated" directory

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127226]
Rename modules to avoid name clobbering

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127227]
Add FastaTable class from DumbView

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127228]
ReferenceEntry now deprecated as well.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127229]
Add a __repr__ for FastaTableRecord

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127230]
Fix tests

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127231]
FastaTable: Get slicing to work right, add tests

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127232]
FastaTable: do not use contig name in fai file, as `samtools faidx` may mangle it

[Fixes bug 23974]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127246]
   bug 23893 - add fai test file to pbcore's package_data	

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127254]
pbcore: version in 2.2 is now 0.8.0

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127329]
   Bug 23925. Same as change 127376, but file locations have changed in mainline. Change zmw 9 in the ccs.h5 test data to have HQ region > 0 but NumEvent == 0. Ensure that it doesn't show up in sequencingZmws.

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127377]
Merge FastaTable into FastaIO module

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127588]
   Bug 24029. Let ungappedPulseArray handle uint32s.	

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127590]
Basic FofnReader class

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127628]
BasH5Collection effectively working now

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127629]
Remove disused method

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127696]
Enable attaching a FOFN of input movies to the CmpH5Reader

... at which point you can get a Zmw or ZmwRead cursor into the
relevant bas/bax file using aln.zmw or aln.zmwRead.

This is a work in progress but is already useful.

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127697]
FofnReader -> readFofn ... having a reader class was overkill

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127761]
Whitespace cleanup

[Tracking bug 23893]

[git-p4: depot-paths = "//depot/software/bioinformatics/lib/python/pbcore/": change = 127762]