I'm trying to produce a simple window => coverage table from a bam file. I produced (non-sliding) windows with `bedtools makewindows` and then ran `bedtools coverage -abam alignment.bam -b reference.windows > coverage`. The problem is that I cannot make sense of the output I got. Here's a sample:

```
I    0    215    SRR1297046.176411/2    23    +    0    215    0,0,0    1    215,    0,    1    215    215    1.0000000
I    0    216    SRR1297046.2210768/1    23    +    0    216    0,0,0    1    216,    0,    1    216    216    1.0000000
I    1    222    SRR1297046.178368/1    24    +    1    222    0,0,0    1    221,    0,    1    221    221    1.0000000
```

The first field is the chromosome name and the fourth one is the read's, but what are the others? This output is inconsistent with the ones described [here][1]. How can I convert this output into a "window => coverage" table?

I'd appreciate any help.

 [1]: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html?highlight=coverage
<p>If you want the coverage of each entry in <code>reference.windows</code> then <code>bedtools coverage -a reference.windows -b alignment.bam &gt; coverage</code> is what you want.</p>

<p>BTW, this will probably double count overlapping paired-end reads. You could alternatively use <code>samtools depth</code> with some post-processing and not have to worry about that.</p>
