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itmat / rum

RNA-Seq Unified Mapper
http://cbil.upenn.edu/RUM
MIT License
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question on output file #141

Open e-manduchi opened 11 years ago

e-manduchi commented 11 years ago

Quick question: the RUM_Unique and RUM_NU file output from release > 2 are sorted by location, correct? At least, so it appears from a quick look at the code. In previous release those were the files called RUM_Unique.sorted and RUM_NU.sorted. Just wanted confirmation.

greggrant commented 11 years ago

That appears to be correct, they are now sorted by location by default and no longer are the files present that are sorted by id number.

On Tue, 16 Oct 2012, e-manduchi wrote:

Quick question: the RUM_Unique and RUM_NU file output from release > 2 are sorted by location, correct? At least, so it appears from a quick look at the code. In previous release those were the files called RUM_Unique.sorted and RUM_NU.sorted. Just wanted confirmation.

Reply to this email directly or view it on GitHub: https://github.com/PGFI/rum/issues/141

mdelaurentis commented 11 years ago

I don't think there's a particular reason I omitted the files that are sorted by read id (RUM_Unique.sorted and RUM_NU.sorted). I think I may have just not included them because they weren't listed in the original RUM user guide. I believe I thought they were intermediate files that weren't necessary in the final output. I can add them back pretty easily if you want.

safisher commented 11 years ago

Why not keep the sorted versions and remove the unsorted versions?

On Oct 16, 2012, at 4:20 PM, Mike DeLaurentis notifications@github.com wrote:

I don't think there's a particular reason I omitted the files that are sorted by read id (RUM_Unique.sorted and RUM_NU.sorted). I think I may have just not included them because they weren't listed in the original RUM user guide. I believe I thought they were intermediate files that weren't necessary in the final output. I can add them back pretty easily if you want.

— Reply to this email directly or view it on GitHub.

e-manduchi commented 11 years ago

I think things got confused. In my original message I noted that the files currently called RUM_Unique and RUM_NU appear to be sorted by location, which was confirmed by Greg. These files were those previously called RUM_Unique.sorted and RUM_NU.sorted. What's no more are the files previously called RUM_Unique and RUM_NU which used to be sorted by id (and were not sorted by location).

e-manduchi commented 11 years ago

I'm not sure there is a need for the files sorted by read ids.