bli25wisc/RSEM — pull request #6 by syounkin (2014-03-17 16:34:06+00:00)
Title: Fixed (Non-Random) Seed for 'rsem-simulate-reads'

My goal was to create a version of rsem-simulate-reads that uses a fixed seed. We are using the simulator for some work here at UW-Madison, but in order to ensure reproducibility we needed a way to fix the seed in rsem-simulate-reads.

I accomplished this by adding a few lines to the makefile, and creating two header files.

The header files are identical except for how they treat the seed for the random number generator.

Now, during make, rsem-simulate-reads-fixed-seed is created using the alternative header file simul-fixed-seed.h.

The file simul-random-seed.h exists as a placeholder for the original simul.h file.

Certainly there is a better way to include fixed seed functionality, but I thought you might be interested in this solution in the short term.

All simulators should have the ability to fix the seed, and I encourage you to incorporate fixed seeds into your program.

We appreciate RSEM very much, and are grateful that the source was available on Github.

I look forward to your comments.

Thanks,

Sam
UW-Madison
Department of Biostatistics and Medical Informatics
Kendziorski Group