v1.2.14: Add support for bowtie2 indices as input

⚠️ Intoduces non-backwards compatible changes to the CLI:

• Option -m, --minimap2 becomes -a, --aligner, taking either "minimap2" or "bowtie2" as value
• Option -f, --fasta becomes -g, --genome

Changes in behaviour:

• -g must be a fasta file when using minimap2, and a bowtie2 index prefix when using bowtie2
• A fasta file is created among temporary file when using bowtie2. It is generated from the bt2 index.

v1.2.11

fix bug that caused read skipping when entries are missing from one i…