Update pbalign cram tests because of blasr SDPAlign change 134507.
bug 24413

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 134614]
Add hitPolicy=leftmost to pbalign. Add cram tests.
bug 25215	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135005]
Update testdata (fofn) for pbalign.
bug 24733	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135013]
Update temp file manager so that pbalign won't raise an error when usrs 
have no write permission to '/tmp'.
bug 25215

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135014]
Update pbalign's cram test because blasr has been modified.
bug 24437	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135411]
Update pbalign's cram tests accordingly (because of change 135710 to blasr).
bug 25290 

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135923]
bug 25014 avoiding the missed integration message...

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 135961]
bug 25378 - refactor pip-install rules and remove duplicate virtualenv.py

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 136724]
Fix bug 25423: (maskAlignedReads fails on empty cmp.h5)

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 136964]
Remove pseudo namespace pbtools from pbalign.
Change program name from 'pbalign.py' to 'pbalign'.
Change python api accordingly ('from pbalign.pbalignrunner import PBAlignRunner')
Update cram/unit tests.
bug 24835

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 137063]
Update maskAlignedReads (import from pbalign instead of pbtools.pbalign)
bug 24835	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 137112]
       loadChemistry changes:

       - work on a list of bas files in addition to just a fofn
       - print out usage on invalid command line

       [Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 137515]
       Fix pbalign repack issue I observed.  Fix found by yli.

       [Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 137516]
Fix loadChemistry, sorry for the mixup

[Tracking bug 24842]

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 137539]
Enable pbalign to map very short reads using simple params (e.g., 
pbalign in.fa ref.fa out.sam --minLength 10)
bug 25361	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 138342]
bug 25532 - major relocation batch, this will break a lot of jenkins builds,
I will fix it and triage the fix on Monday.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 138434]