#90 Bug in percolator rank

[William S Noble]

I ran a simple experiment using tide-index + tide-search + percolator, and I noticed that the ranks of the top-ranked and bottom-ranked PSMs in the percolator.target.psms.txt file were swapped. There are 117 PSMs total, and the best-scoring one appears first in the file but has a rank of 117. Then the ranks go 2-116, and then the worst-scoring PSM has a rank of 1. Weird!

The input and output files are attached. You can reproduce this behavior by doing an svn update in crux/trunk/doc/user and then running demo1.sh in the demos subdirectory.

[Kaipo]

Strangely I haven't been able to reproduce this. I tried running the demo script, with the target/decoy tab delimited inputs, and with the pin.xml input.

[William S Noble]

I also could not reproduce it on Linux, but I have since reproduced it on a different Mac. It seems that the difference may be due to differences in the sort order of the tide-search.{target,decoy}.txt input files. Let's wait till Charles gets the smoke tests to pass on MacOS (Issue #40) and then revisit this one. I'll assign it to me, since it needs a Mac to check whether the problem persists.

[William S Noble]

I just verified that this one is still a problem on MacOS.