Fix problem in plotLodProfile if max lod is at multiple locations
Add a couple of args to plotLodProfile, incl showallchr
Fix problem in write.cross.csv: was giving wrong genotype labels for ril

  - was giving A/H rather than A/B; similar problem for other cross types
Had the wrong argument name in the help file for plotLodProfile
Add to TODO list
Fix a problem in refineqtl/stepwiseqtl re map attr to qtl object

 - If the qtl object got recreated but the cross had been subsetted (by
   chr), the map attribute would have only the subset of chromosomes.
Make require.fullrank=FALSE the default except in stepwiseqtl
Add reduce2grid() for subsetting calc.genoprob results to a grid
Fix comment within the reduce2grid function
Another simplification in reduce2grid
More meaningful names within reduce2grid()
Export some more functions to NAMESPACE, for use by funqtl
fixed valgrind problem in init_stepf
Merge branch 'master' of git://github.com/byandell/qtl into brian
Update version and date; add change to STATUS
Small changes to eliminate compiler warnings
Fix bug in summary.scantwo re re-ordering of chr factor levels