Long run time with large assembly and many contigs
Hi,
I am trying to run mosdepth like this:
```
export MOSDEPTH_PRECISION=6
mosdepth --fast-mode \
         --by <assembly.fa.bed3> \
         --threads 4 \
         --thresholds 1,10,30 \
         <assembly.fa> \
         <mapping.bam>
```
on metagenomes but the runtime is exceeding two days, so I cant complete the jobs on my regular cluster nodes.
They do have many (short) contigs, e.g.:
```
> seqkit stats <assembly>.fa
file           format  type   num_seqs        sum_len  min_len  avg_len  max_len
<assembly>.fa  FASTA   DNA   2,041,321  1,499,035,773      200    734.3  372,868
> wc -l <assembly>.fa.bed3                             
2041321 <assembly>.fa.bed3

```
WGS and RNA-seq mapping stats:
```
> samtools .../mg.reads.sorted.bam
165453111 + 0 in total (QC-passed reads + QC-failed reads)
...
149618292 + 0 mapped (90.43% : N/A)
...
> samtools flagstat .../mt.reads.sorted.bam
147055988 + 0 in total (QC-passed reads + QC-failed reads)
...
147055988 + 0 mapped (100.00% : N/A)
...
```
Is this expected? Could it be related to #56 or #71? I dont have any memory issues so far though.

The same also happens when supplying a bed with genes for `--by`:
```
> cut -f 4 genes.bed | wc -l
3009287
> head genes.bed
contig_001   156     318     gene_0079        0       +       156     318     0       1       162,    0,
contig_002   2       167     gene_0080        0       -       2       167     0       1       165,    0,
contig_003   1       304     gene_0081        0       +       1       304     0       1       303,    0,
contig_004   145     331     gene_0082        0       -       145     331     0       1       186,    0,
contig_006   1       298     gene_0083        0       -       1       298     0       1       297,    0,
contig_009   2       167     gene_0084        0       -       2       167     0       1       165,    0,
contig_010   2       299     gene_0085        0       +       2       299     0       1       297,    0,
contig_012   1       358     gene_0086        0       -       1       358     0       1       357,    0,
contig_013   0       258     gene_0087        0       +       0       258     0       1       258,    0,
contig_013   274     352     gene_0088        0       +       274     352     0       1       78,     0,
```

Best 

Oskar
