bug 24050 - remove all pip related conditionals from the master Makefile
pbcore/GenomicConsensus/kineticsTools/pbaha/pbalign/pbbarcode/pbh5tools/pbsamtools

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130184]
   pbalign now supports gmap.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130282]
   add unit test for pbalign.py --algorithm gmap
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130283]
   Enable '--filterAdapterOnly' option in pbalign. This option is only used by
   the 11k_Unrolled_Resequencing.1.xml protocol to filter reads that maps to 
   adapter regions.
   Add unit tests and a cram test.
bug	24093

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130436]
   Handle exceptions when failed to read the input cmp.h5 (e.g., a cmp.h5 
   with no alignment).
bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130488]
   Update log info for 'pbalign.py --algorithm=gmap'.
   bug 22808	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130498]
bug 24050 - refactoring regarding pip-install

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130546]
bug 24050 - bad idea to redirect fd in Makefile, not robust.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130550]
   Add an experimental option --pulseFile, which enables users to 
   specify a fasta file as input and generate a cmp.h5 file with
   pulse metrics loaded. This option only works when algorithm is 
   gmap, and --forQuiver is specified. Support for blasr remains TBD.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130586]
Sort files in fofn.	
bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130599]
bug 21591
   ensure that all regions produced by the python APIs are sorted 
   (filter and maskAlignedReads) as produced by python code. 
   remove unsorted rgn.h5 from mask_aligned_reads cram test which breaks
   the new assert. all unit tests for pbfilter and pbalign pass as well
   as Mapping core test.

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130641]
Support --pulseFile when algorithm is blasr, ex:
pbalign.py reads.fa ref.fa out.cmp.h5 --forQuiver \
--pulseFile reads.fofn
bug 22808	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130746]
   Add a cram test for pbalign --pulseFile when algorithm is blasr.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130748]
   Temporary files and intermediate files are no longer saved unless
   a hidden option --keepTmpFiles are specified.
   pbalign will be more space efficient for resequencing jobs such as 
   the 45X human resequencing job. 
   bug 22808	

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 130797]