new hmm_ft, mods to calc_genoprob in hmm_main need to be moved out
make cross scheme arg to calc_genoprob; move cross temps to static
forgot to add cross_scheme to hmm_main.h and modify hmm_ft.h
Updated the MQMscan function to also provide cim.covar structure, so we can use this to plot selected covariates under the scanone plot
Merge branch 'master' of http://github.com/kbroman/qtl
Also when there are no intermediate markers requested
Update version.
Merge branch 'master' of git://github.com/byandell/qtl into BCsFt
Subtle changes to new_multiqtl.pdf; add new_multiqtl.R (the code).
Merge branch 'master' into BCsFt
Subtle changes to new_summary_scanone.pdf and new_summary_scantwo.pdf; add .R files.
Update STATUS file
Merge branch 'master' into BCsFt
Update version.
Add Arends et al reference to standard_references.txt; update MQM.Rd with this.
Merge branch 'master' into BCsFt
Merge branch 'master' of git://github.com/kbroman/qtl
Merge branch 'BCsFt' of git://github.com/kbroman/qtl
Updated cross_scheme on all functions; need to do step_ftb now
Slight change to top.errorlod so that the output columns are character strings not factors.