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cole-trapnell-lab / cufflinks

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Cuffquant "usage" information is wrong --- it's the instructions for cuffdiff instead of cuffquant #24

Closed alexgraehl closed 9 years ago

alexgraehl commented 9 years ago

Line 91 in : https://github.com/cole-trapnell-lab/cufflinks/blob/master/src/cuffquant.cpp

It gives the usage information for cuffDIFF, not cuffQUANT. In particular, it says that cuffquant supports multiple different BAM/SAM samples, comma-delimited which appears not to be the case according to the help on the web.

cbrueffer commented 9 years ago

This was fixed in 361b704c28eb9e5eb2b6381076c04b286226aea1 in the develop branch in December 2014, but has not been merge back to master yet.

ctrapnell commented 9 years ago

I’m planning on a new release that pushes out this an many other fixes, large and small, soon.  I’ve been on a grant writing and travel bender, but the rest of the summer is more free.  It’s also taken me a while to move my integration test suite from Harvard to UW, but that’s mostly up and running now.  Stay tuned.

Cole Trapnell, Ph.D.Assistant Professor

Department of Genome Sciences

University of Washington

On Mon, Jun 29, 2015 at 4:36 AM, Christian Brueffer notifications@github.com wrote:

This was fixed in 361b704c28eb9e5eb2b6381076c04b286226aea1 in the develop branch in December 2014, but has not been merge back to master yet.

Reply to this email directly or view it on GitHub: https://github.com/cole-trapnell-lab/cufflinks/issues/24#issuecomment-116622872

alexgraehl commented 9 years ago

Awesome! I'll be installing it as soon as it's ready!

Alex

On Jun 30, 2015, at 6:50 PM, Cole Trapnell notifications@github.com wrote:

I’m planning on a new release that pushes out this an many other fixes, large and small, soon. I’ve been on a grant writing and travel bender, but the rest of the summer is more free. It’s also taken me a while to move my integration test suite from Harvard to UW, but that’s mostly up and running now. Stay tuned.

Cole Trapnell, Ph.D.Assistant Professor

Department of Genome Sciences

University of Washington

On Mon, Jun 29, 2015 at 4:36 AM, Christian Brueffer notifications@github.com wrote:

This was fixed in 361b704c28eb9e5eb2b6381076c04b286226aea1 in the develop branch in December 2014, but has not been merge back to master yet.

Reply to this email directly or view it on GitHub: https://github.com/cole-trapnell-lab/cufflinks/issues/24#issuecomment-116622872 — Reply to this email directly or view it on GitHub https://github.com/cole-trapnell-lab/cufflinks/issues/24#issuecomment-117390695.

dsenalik commented 8 years ago

The develop branch of cuffquant.cpp still lists "-c/--min-alignment-count" as an option in the usage (line 107), but there is no code to handle this option This issue is closed so I will open a new one (#57)