Record of Changes to LAMP
Fixed a bug in printing of allele frequencies for direct association
tests with --dominant or --recessive options. With older versions,
information in detailed log files is correct, but frequencies printed
to the screen can be incorrect.
Fixes a bug in version 0.0.8. When testing only for association,
version 0.0.8 outputs a summary of the fitted model to the screen
(including allele frequency and penetrances). When the disease
allele frequency or penetrance is estimated as 1.0, it is printed
incorrectly as .1000 -- this is now fixed.
Added a --prefix option to allow the name of detailed output files
to be controlled by users.
Renamed the option --unrelateds-and-trios to --ignore-linkage. The
new name emphasizes that this option does not ignore pedigree
structure -- rather, it simply does not attempt to fit models
that rely on linkage information. The option is convenient
when the intent is mainly to test for association, such as in the
first pass of whole genome association scan analysis.
Added a --swap option to reduce memory use in datasets that include
Fixed bug that caused crash when "testing" monomorphic markers for
association. Although monomorphic markers will not display evidence
for association, they also should not cause a crash!y
New tutorial and examples.
Improved performance for datasets consisting of unrelated, trios
or other small sibships.
Improved code for auto-detecting family configurations.
Fixed lambda(S) calculation for indirectly associated markers.
Fixed bugs in the handling of some extended pedigrees.
First public release.