Disagreement of results with samtools and bedtools
Dear,

We have being testing the performance of mosdepth and we came across with some disagreement that we are not able to explain.

The mean depth (calculated with per-base file in ROI region) is below the value that we get with bedtools and samtools. These last two tools agree one to each other. To make sure that we are certainly adding the alignments that we want, first we select them with samtools  view (-Q20 -F4).

The difference is bigger as the mean depth of the sample raises.

We have tuned the tool with the parameters of quality and the off of some bam flags with no success 

For some reason, mosdepth does not sum certain aligmnents but we can't guess the criteria.

Can someone help us?

some of the results are:

sample | Depth (bedtools genomecov) | Depth Mosdepth Q20 -F4 | Diff
-- | -- | -- | --
S1 | 226.35 | 140.17 | 86.18
S2 | 282.6 | 201.94 | 80.66
S3 | 22.1 | 13.59 | 8.51
S4 | 321.53 | 232.04 | 89.49
S5 | 302.2 | 200.68 | 101.52
S6 | 463.69 | 309.07 | 154.62
S7 | 1712.59 | 1218.7 | 493.89
S8 | 283.97 | 193.77 | 90.2
S9 | 565.61 | 384.24 | 181.37
S10 | 318.84 | 228.56 | 90.28
S11 | 498.36 | 330.7 | 167.66
S12 | 1023 | 719.74 | 303.26
S13 | 1084.31 | 759.14 | 325.17
S14 | 263.12 | 187.77 | 75.35
S15 | 288.81 | 209.73 | 79.08
S16 | 883.44 | 643.81 | 239.63
S17 | 572.41 | 434.08 | 138.33
S18 | 1423.13 | 1046.05 | 377.08

In addition, we have checked the results base by base and the difference with respect to IGV is clear. The example shows a base that is 1165X and mosdepth output is 828X:
![screenshot from 2018-09-05 12-20-49](https://user-images.githubusercontent.com/41467687/45214556-106c2d00-b29b-11e8-99da-ab04f9811c61.jpg)





