update miRli analysis for bedtools

[broughtonjp]

analyze_miRli.scala uses -nms and -scores for mergeBam. However, these commands are depreciated for bedtools 2.22 and need to be updated to the new bedtools merge that uses -c and -o.

case class mergeBam(@Input bamFile: File, @Output mergedBed: File) extends CommandLineFunction{

    override def shortDescription = "mergeBam"
    def commandLine = "bamToBed -i " +
    required(bamFile) +
    " -splitD |mergeBed -i stdin -nms -s -scores max > " +
    required(mergedBed)

}

[olgabot]

Looks fine to me! I don't use miRli so can't comment much on this. Do you have a PR you're working on with the changes?

[gpratt]

Do you need someone to fix this for you James or do you think you can figure it out yourself? On Mar 18, 2015 2:16 PM, "Olga Botvinnik" notifications@github.com wrote:

Looks fine to me! I don't use miRli so can't comment much on this. Do you have a PR you're working on with the changes?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/64#issuecomment-83181853.

[gpratt]

Post the expected output from the working version of the run if you need help.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Thu, Mar 19, 2015 at 1:33 PM, Gabriel Pratt gpratt@ucsd.edu wrote:

Do you need someone to fix this for you James or do you think you can figure it out yourself? On Mar 18, 2015 2:16 PM, "Olga Botvinnik" notifications@github.com wrote:

Looks fine to me! I don't use miRli so can't comment much on this. Do you have a PR you're working on with the changes?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/64#issuecomment-83181853.

[broughtonjp]

I think that it should be: Old: mergeBed -i stdin -nms -s -scores max

New mergeBed -i stdin -s -c 4,5,6 -o distinct,max,distinct

Does this look correct?

[gpratt]

yah, that looks perfect. Double check the output of the bed files just to confirm.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Thu, Mar 19, 2015 at 1:36 PM, James Broughton notifications@github.com wrote:

I think that it should be: Old: mergeBed -i stdin -nms -s -scores max

New mergeBed -i stdin -s -c 4,5,6 -o distinct,max,distinct

Does this look correct?

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/64#issuecomment-83754076.

[broughtonjp]

Okay, I'll run a test once my current queue clears on TSCC

[gpratt]

don't do that, just try it one one sample.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Thu, Mar 19, 2015 at 1:39 PM, James Broughton notifications@github.com wrote:

Okay, I'll run a test once my current queue clears on TSCC

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/64#issuecomment-83754645.

[broughtonjp]

okay seems to work

[gpratt]

Perfect. Make the update and run all that ish through.

Gabriel Pratt Bioinformatics Graduate Student, Yeo Lab University of California San Diego

On Thu, Mar 19, 2015 at 1:55 PM, James Broughton notifications@github.com wrote:

okay seems to work

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/gscripts/issues/64#issuecomment-83758100.