Sort a BAM file by chromosome and position, keeping the index and read names
out of the way. Always write to a new file: `samtools sort` refuses to
overwrite its input.

```bash
samtools sort -@ 2 -o sorted.bam in.bam
samtools index sorted.bam
samtools quickcheck -v sorted.bam
```

For long reads the memory footprint grows with the number of reads in flight,
so `-@` buys speed but not memory. When the machine is small, drop it:

```bash
samtools sort -o sorted.bam in.bam
```

`samtools quickcheck -v` prints nothing when the file is intact, which makes it
easy to use in a pipeline with `set -e`.