initial check for DAG based consensus code for general consensus and haplotyping / consensus

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109656]
   add command cram test cases

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109809]
   these files should not be submitted..

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109810]
   fix a bug for reference base consensus

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109812]
   fix / add tests

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109813]
   add command option processing

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109814]
   make the style match PEP 8 as much as possible

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109815]
   add output option for the dag

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109816]
   output lower case for weak consensus base

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109817]
   add LICENSE/Makefile, change file type to kxtext

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109818]
   make dag data dump prettier

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109819]
   fix a minor bug

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109820]
re-format the description 

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109821]
   more cosmetic tweaks

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109822]
   remove un-necessary finding_best_template_by_blasr for subgroup

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109826]
Use FastaReader API (change in pbcore).

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109891]
Per discussions, move the following projects to a new staging/ directory,
to warehouse projects that are not yet or no longer used in production 
code: 
	pbsmrtcellqc
	pbsmvd
	pbaligntools
	pbdagcon

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 109950]
   get ready for posting it to github for HGAP reference implementation bug #21512

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 115421]
   add the Cython version of quick-consensus code
      Not a bug #120472

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 120472]
   make q-sense functions can be called as module
   Bug #21512

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbdagcon/": change = 121208]