v1.2.0

Added

• Add -k / --max-hits N to cap Bowtie2 alignments per read.

• Add --all-hits (alias --full) to report all Bowtie2 alignments (-a), as earlier versions did.

• Keep the Bowtie2 alignments as BAM files in <tmpdir>/bowtie/, written with --no-unal (unaligned reads are left out), so thresholds can be revisited without remapping. Use --no-bam to skip them.

Changed

• Add Read the Docs documentation (user guide, database, analysis, outputs, limitations, development) and shorten the README to point to it.
• Bowtie2 now reports at most 200 alignments per read by default (-k 200). Benchmarks showed 0-1.1% of read assignments changing, unchanged detected taxa, and a much faster, lighter mapping step. Use --all-hits for the previous behaviour; results can differ slightly from 1.1.x otherwise.
• The mapping step requests more memory (6x instead of 3x the input size) and time (3x) under --all-hits, since uncapped runs ran out of memory or time at the capped request.