Reported coverage is different from alternative tools
Hi Brent,

We were using mosdepth to estimate the average coverage in our whole exome sequencing samples, and it didn't sum up with what we expected from napkin calculations using simply the reads number and length. 

So I tried other tools to do the calculation (`samtools depth`, `sambamba depth`, `qualimap`) and got a result much closer to what I expected. All those tools agree with each other but not with mosdepth. I made a small test case that demonstrates the difference, here are the results:

samtools depth (v1.10):

```
$ samtools depth test.bam -a -b test.bed
chr13   32315631        579
chr13   32315632        580
chr13   32315633        582
chr13   32315634        581
chr13   32315635        573
chr13   32315636        574
chr13   32315637        573
chr13   32315638        575
chr13   32315639        575
chr13   32315640        576
```

sambamba depth (v0.6.8):

```
$ sambamba depth base test.bam -L test.bed
REF     POS     COV     A       C       G       T       DEL     REFSKIP SAMPLE
Processing reference #13 (chr13)
chr13   32315630        581     0       0       0       566     2       0       SBJ00491_TGX141015_L2000210
chr13   32315631        580     0       1       0       572     0       0       SBJ00491_TGX141015_L2000210
chr13   32315632        582     578     0       0       0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315633        581     0       578     0       0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315634        573     0       0       0       568     0       0       SBJ00491_TGX141015_L2000210
chr13   32315635        574     0       573     0       0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315636        573     0       570     0       0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315637        575     0       0       570     0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315638        575     2       0       566     0       0       0       SBJ00491_TGX141015_L2000210
chr13   32315639        576     0       572     0       0       0       0       SBJ00491_TGX141015_L2000210
```

qualimap (v.2.2.2-dev):

```
qualimap --java-mem-size=50G bamqc -bam test.bam -outdir qualimap_test -gff test.bed
$ grep "mean coverageData" qualimap_test/genome_results.txt
mean coverageData = 577X
```

However, mosdepth (v0.2.9) reports a significantly lower coverage:

```
$ mosdepth test_mosdepth test.bam --by test.bed
$ zgrep chr13 test_mosdepth.per-base.bed.gz | grep 32315630 -A 10
chr13   32315628        32315630        333
chr13   32315630        32315632        332
chr13   32315632        32315633        334
chr13   32315633        32315634        336
chr13   32315634        32315635        328
chr13   32315635        32315637        329
chr13   32315637        32315639        328
chr13   32315639        32315640        329
chr13   32315640        32315641        327
chr13   32315641        32315647        328
chr13   32315647        32315648        327
chr13   32315648        32315650        325
```

Trying to see if it's because of filters on read flags/qualiaty. As far as I understand, by default mosdepth includes all reads with mapping quality >=0, so that's not that. For flags, trying to keep only mapped reads:

```
$ mosdepth -F4 test_mosdepth_mapped test.bam --by test.bed
$ zgrep chr13 test_mosdepth_mapped.per-base.bed.gz | grep 32315630 -A 10
chr13   32315628        32315630        333
chr13   32315630        32315632        332
chr13   32315632        32315633        334
chr13   32315633        32315634        336
chr13   32315634        32315635        328
chr13   32315635        32315637        329
chr13   32315637        32315639        328
chr13   32315639        32315640        329
chr13   32315640        32315641        327
chr13   32315641        32315647        328
chr13   32315647        32315648        327
chr13   32315648        32315650        325
```

Gives the same result.

Eyeballing in IGV gives the depth of ~580x, matching other tools.

I'm just wondering if I'm missing anything in how mosdepth is working? Would really appreciate help!

Attaching the test BAM/BED files.
[test.tar.gz](https://github.com/brentp/mosdepth/files/4699408/test.tar.gz)


Vlad

cc @ohofmann 