Fixes for transcriptome and metagenome modes

[lcoombe]

• Fix missing aligner variable in metagenome mode
• Fix return value when q_mode is True for function primary_and_unaligned_chimeric in get_primary_sam.py
• Check for and skip secondary alignments in base quality characterization
• If the homopolymer length modelling doesn't converge, detect this and raise a more informative error
• Remove --chimeric from transcriptome characterization to keep consistency with simulation options
• Remove homopolymer characterization/simulation from metagenome mode
  • In many tests, there wasn't enough data for the model to converge, leading to errors
  • The options are still available for advanced users, just will not be advertised in the help page