Merge branch 'staging' into tmp

Conflicts:
	src/recomb.cpp
codequality model.h
Merge branch 'staging' into mjh-contrib

Conflicts:
	src/arg-sample.cpp
Merge branch 'staging' into mjh-contrib

Conflicts:
	src/compress.cpp
	src/parsing.h
Merge branch 'staging' into mjh-contrib
remove small diff
Revert "first cut at sampling phasings"

This reverts commit 34ea4d20885c03de906134749068d54cc7d7b87d.

Conflicts:
	src/arg-sample.cpp
	src/model.h
Merge branch 'master' into mjh-contrib
simplify writing local trees as bed
changed tabs to spaces
removed postnodes from Tree.h and some tabs->spaces
small changes to tabix.cpp,tabix.h
some changes to arg-summarize.cpp and Tree object:
-move SPR out of Tree object
-some bug fixes to arg-summarize to stop crashing at end and handle memory better
-use Config object for command-line objects
Merge branch 'mjh-contrib'

Conflicts:
	src/compress.cpp
	src/model.h
	src/tabix.cpp
fixed error in previous merge