Load metric "SubstituionTag" to out.cmp.h5 with --forQuiver.
   Add option "--byread", which, if specified, may load pulse info to
   out.cmp.h5 faster when the number of alignments is small.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 126792]
   Change default metrics to load for quiver to:
       InsertionQV, SubstitutionQV, DeletionQV, DeletionTag, MergeQV
   Add --metrics option so that users can specify the pulse metrics that they
   want to load instead of using the default metrics.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 126802]
   Update unit tests for pbalign.
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 126829]
   Update pbalign.py so that it can load pulse info from ccs to a cmp.h5 (e.g.,
   pbalign.py *.ccs.h5 ref.fa out.cmp.h5 produces the same output as 
   pbalign.py *.bas.h5 ref.fa out.cmp.h5 --useccs="useccsdenovo")
   bug 22808

[git-p4: depot-paths = "//depot/software/bioinformatics/tools/pbalign/": change = 126850]