BamConfig / FastqWriter changes:

BamConfig:
    - library_config_by_{index,name} both renamed to library_config
    - no longer tries to open fastqs
    - now prints a warning if data from one config line overrides data
      from another
    - decoupled from Options, now takes int cutoff_sd directly

FastqWriter:
    - now takes library name and a flag (is_read1) instead of an
      explicit path.
    - now throws if unable to open an output file.
    - an attempt to open all files is made in the BreakDancer
      constructor.