General changes:

• Fix return value when q_mode is True for function primary_and_unaligned_chimeric in get_primary_sam.py (#230)
• Check for and skip secondary alignments in base quality characterization (#230)
• If the homopolymer length modelling doesn't converge, detect this and raise a more informative error (#230)
• Fixes for -min and -max parameters (#234)
• Refactoring

genome mode:

• Fix to avoid IndexError being raised with some parameter combinations when simulating genomic reads (#232)

transcriptome mode:

• Remove --chimeric from transcriptome characterization to keep consistency with simulation options (#230)

metagenome mode:

• Fix missing aligner variable in metagenome mode (#230)
• Remove homopolymer characterization/simulation from metagenome mode (#230)
• Fix for simulating abundances in metagenome mode (#232)