Incorrect Downstream annotation bug in annotatePeak

[ikumar2000]

There seems to be a bug while using annotatePeak with ingoreUpstream=TRUE. Many peaks show up annotated as "Downstream (<=300)" however they are not. They are not even downstream of the associated gene. The distanceToTSS show up correct though with -ve value indicating that the peak is upstream (and intergenic). In some other cases, the peaks are annotated as "Downstream (<=300)", even if the distance to the associated gene is much more that. Note: this issue is not there when using ignoreDownstream=TRUE or not using this parameter at all.

[GuangchuangYu]

can you provide a simple example to demonstrate this issue?