v0.2.0-alpha6

• Fix bug in dense output mode, and make it the default output mode (Thanks to Steven Robbins for bug report)
• Change help messages so default is to have short colourful output
• Speed up when mapping due by running samtools sort in a temporary directory
• filter: Introduce --inverse for decontamination uses
• covered_bases and reads_per_base are new coverage statistics (methods)
• When running in genome mode and mapping, genomes are concatenated automatically so -r isn't required
• In genome mode, when a genome has too small a coverage for --min-covered-fraction, reads mapped to that genome are not counted as mapped when calculating relative abundance (same for contig mode).
• Filtering options now have -read to reduce potential confusion
• Other small bug and documentation fixes