[FIX] Fixing initialization issues in edit environment iterators.
[FIX] Fixing misuse of append => appendValue() in rep_sep.
[FIX] Using string literal instead of string in gustaf.
[FIX] Fixing a replace() that uses a single element as the source.

Also, whitespace reformatting. The change is only in the "if (j != i)"
branch.
[FIX] Removing usage of elements-are-container feature.
[FIX] Member initialization in graph_impl_hmm.h.

Also, white space changes. The only semantic change is in initializing
data_begin and data_end in the default constructor.
[FIX] Missing member initialization in mason_variator.cpp.
[FIX] Member initialization in misc_interval_tree.h.
[FIX] Fixing issue with empty BAM files and bam_library_size demo.
[FIX] For previous change in graph_impl_hmm.h
[FIX] Marking unused variable explicitely as such.
Merge pull request #59 from holtgrewe/feature/bug-fixes

Fixes to various non-obvious bugs