Coverage Mapping Issue

[ChaochihL]

Type of issue

• [x] Bug
• [ ] Feature request

---

Bugs

Have you looked at the wiki?

The wiki is located here

• [x] Yes
• [ ] No

  Which handler are you having trouble with?

Coverage Mapping

Describe your problem

Coverage Mapping currently does not support BED files as input. It currently only plots for GFF files.

What is the error message being generated?

# Put your error message here

Copy the part of the config file used by this handler

#   Shared values go here

#   Handler-specific values go here

#   Dependency definitions go here

Has anyone else been able to replicate your error?

• [ ] Yes
• [ ] No

---

Feature requests

What new thing is being added?

• [ ] New handler
• [ ] Modification to handler

  Describe the changes made

  Where does this fit in with the existing pipeline?

  List any dependencies that will be needed for this change, providing links to the source code as needed

  Do you have a script for this change? Please note that we can implement your code faster if you write everything as BASH functions.

• [ ] Yes
• [x] No

If yes, please make sure the code is posted online and link to it below:

name of code exerpt

Good hosting sites are GitHub and GitHub Gist.

Thank you for your help improving sequence_handling!

[pmorrell]

I also go not output in '/CoveragePlots'. I found the following error message repeated in the output file:

Collecting sample names...
Mapping coverage...
Finding coverage histograms...
Plotting coverage...
Creating R Library at /panfs/roc/groups/9/morrellp/pmorrell/Apps/PHoffman/sequence_handling/.RLibs 
Failed to install Hmisc 
Error in FUN(X[[i]], ...) : there is no package called 'Hmisc'
Calls: main -> batchInstall -> lapply -> FUN
Execution halted

[Aerin13]

As of commit acc3405, Coverage_Mapping now accepts BED files as valid regions files. Coverage plotting is not currently supported, but is planned for a future version.