Migrate cram test data for blasr and pbalign.
bug 24733 	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 131637]
Bug 24835 - Bug 24050 - refactor the pip uninstall and revise the pbtools pseudoname handling

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 132262]
bug 23997 update with siv reference repo due to failing pssc1 tests
       prop:S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 132429]
Update os.removedir -> shutil.rmtree
bug 22808
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 132747]
Bug 24922. Better error handling for mask_aligned_reads.py.
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 132946]
New chemistry information passing regime: 

chem barcode triple is piped "end-to-end" all the way into the cmp.h5, left to the application level 
to be decoded.

This change involves:
 - addition of a new tool "loadChemistry.py" to pbalign, which is responsible for transfering the triple
 - addition of a LoadChemistryService to pbalign that is run under --forQuiver
 - fixing pbalign tests
 - get SMRTpipe mapping modules to do loadChemistry.py as part of loadPulses step
 - cmph5tools merge needs to properly merge new columns in MovieInfo table

[Bug 24737]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133135]
       Fix pbalign cram test

       [Bug 24737]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133181]
Bug 24922. Handle case where the control cmp.h5 file has no aligned reads.
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133183]
bug 24325	
port extractUnmappedSubreads to bioinformatics pbalign.tools

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133504]
Update cram test for pbalign
bug 25062	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133714]
This issue is due to the fact that NFS takes a while to acknowledge/update 
status of a file (from RPC call). The solution is to wait a few seconds and 
try multiple (~5) times to delete a temporary directory; return a warning
instead of an error in case that a temporary directory can not be deleted
with multiple tries.
bug 25074
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133792]
Support files with white spaces in file names.  
bug 25012

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133955]
Migrate pbalign's tests to /mnt/secondary-siv/testdata 
bug 24733	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133994]
Update pbalign's unit test, using datasets in /mnt/secondary-siv/testdata
bug 24733	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 133995]
bug 25012	
Revert from changelist 133955 to 133792
cram tests and unit tests are not reverted, so they will fail util next change.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 134032]
Support input fasta/fofn with white spaces.
bug 25012

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 134043]
Close a temp file created by tempfile.mkstemp() so that NFS does not need to hold
a copy of it after os.remove() is done. This can solve the fundamental NFS lock 
issue.
bug 25074
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 134189]
Fix function isExist so that it does not raise an exception when its
   input file is of type 'None'.
bug 25012	
prop: S2.2

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 134277]