[ensembl-dev] Wiggletools bam coords and coverage mode

[Nathan Johnson]

Morning

I'm just fiddling with the coverage mode and saw what looks like a 1/2 open
issue, or maybe an assumption that bams are using 1/2 open coords.

Samtools show 2 reads starting at 10000:
```
$ samtools view test.bam chr1:1-10000
NB501627:84:HMJNWBGX2:3:22601:21701:15135    121    chr1    10000    0
 49S30M    =    100000    AATAAATTATAGATTATATAAAAATTAATT
AATAATGCTTCCCCTATCCATAACCCTAACCCTAACCCTAACCCTAACC
 //AE//////////EE////////////E///E/////E/////A/////E//////
EEEEEAEEEEEEEEEEEAAAAA
NB501627:84:HMJNWBGX2:3:22601:21701:15135    181    chr1    10000    0    *
   =    100000    AATATTAATTAATTATTATTTAATCGATAA
TATATTAATATTATTTAATCGTATTTAAATTGTTTGTGGTTGTGGGTGAG    EEEE/EEAAEEEE/
EEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAE/<EEE/EEEEEEEEEA/EEEEEA/AAA
```
Tags truncated for brevity.

Wiggletools shows none:
`$ wiggletools seek chr1 1 10000  coverage test.bam`

When extending to 10001, the coverage value only show 1, not 2?
```
$ wiggletools seek chr1 1 10001  coverage test.bam
fixedStep chrom=chr1 start=10000 step=1
1.000000
```

Can someone confirm what's going on here?

Thanks

Nathan
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