omegaMap Bugs and Version Information
What follows is a list of changes to omegaMap source files, executables and documentation that are available for download. Check you have the most up-to-date version by comparing the dates of your files to those contained here.
| Date | Files affected |
|---|---|
| 1st May 2008 | All versions of permute |
| Uncertain base calling, i.e. use of R, Y, N may be interpreted as polymorphism, which adds noise to the LD statistics, and reduces the power of the test for recombination. To avoid this problem, replace the entire column of the alignment with N's when any sequence in that column contains an ambiguous base call. | |
| 30th May 2007 | All versions |
| Bug when using independent model for omega (or rho), with an improper prior, and omegaStart (or rhoStart) is specified using a single value. Avoid this problem by specifying omegaStart (or rhoStart) with a list of values of length L codons (or L-1 codons). Thanks to Marcos Perez-Losada for pointing out this problem. | |
| 19th July 2006 | R functions |
| Fixed a bug in some of the R functions which refused to work when rho_model = constant. Thanks to JL Campos and Jose Andres for pointing it out. | |
| 29th June 2006 | All versions |
| Bug when using log normal prior with block models (omega_model = variable, rho_model = variable). No fix - awaiting new release. Do not use the log normal prior with block models. | |
| 5th May 2006 | Source: omegaMap.cpp. XP: omegaMap.exe |
| Bug fix affecting the way the muStart, etc. options are read from the configuration file. | |
| 19th April 2006 | Documentation: documentation.doc, documentation.pdf |
| When using the improper_uniform or improper_inverse prior, you need to specify the initial value of the parameters using muStart, kappaStart, omegaStart, rhoStart, and/or indelStart. |
