Merge branch 'master' into quoc
Merge pull request #2 from kbroman/master

Think I have X covariates business fixed
Add stepwiseqtlX.R file to the project
Add stepwiseqtlQuoc.R

This is the clean version of stepwiseqtlX with more comments and 1 obsolete function deleted. We can take stepwiseqtlX out of the repo and only work on this file for the code merge. 
4 main functions: countqtltermsQuoc, calcQuoc.penalties, stepwiseqtlQuocv12514, calc.plodQuoc.
Merge branch 'master' of git://github.com/QuocTran/qtl into quoc
Merge branch 'master' into quoc
Remove R/stepwiseqtlX.R
Update version; add Quoc to DESCRIPTION
Rename stepwiseqtlQuoc.R as stepwiseqtlX.R
Rename the stepwiseqtl-related functions for A vs X, using "X" rather than "Quoc"
Remove trailing whitespace
Revise stepwiseqtlX to handle the less-than-full-rank business
Fix the "fix me" bugs in stepwiseqtlX.R
Remove QTLX.Rproj and put in .gitignore
Merge branch 'scantwoperm' into quoc_rev
Revise indentation in stepwiseqtlX.R
Add Quoc Tran to list of contributors in DESCRIPTION
Fix summary.scantwo for the case of X-chr-specific perms and alpha is of length 1
Another fix in summary.scantwoperm
Initial attempt at merging stepwiseqtl/stepwiseqtlX and related calc.penalties functions