Commits

Author Commit Message Labels Comments Date
James Taylor
rp_score_maf.py: improve coordinate handling. Previously output position was the start of the window plus half the window size, which could become inaccurate for windows containing many reference gaps. This now actually calculates the genome position the center of the alignment window corresponds to. Also, skips windows with more than half gaps in the reference (this could result in scores being written for alignment windows corresponding to very small genome windows)
James Taylor
Update README
James Taylor
Adding .hgignore
James Taylor
Import fix for doc_optparse
James Taylor
adding distribute_setup.py
James Taylor
A start toward modernization
James Taylor
Updates for numpy and fixes for more modern Pyrex.
James Taylor
generated code for standard.pyx, fix incompatibility with newer pyrex
James Taylor
Some fixes.
James Taylor
Back to Numeric for the moment, this needs more testing.
James Taylor
Numpy related fixes.
James Taylor
Change all imports to numpy.
James Taylor
Add script to setup (man this is getting annoying)
James Taylor
Genome windowing script.
James Taylor
whoops...
James Taylor
Setup fix.
James Taylor
'rp_adapt_mc.py' is no longer needed.
James Taylor
Another script.
James Taylor
And again...
James Taylor
Fix for setuptools
James Taylor
Updated ez_setup
James Taylor
Adding some core scripts for ESPERR.
James Taylor
Standard model currently has some problems.
James Taylor
Renaming