Changed dependency in src/smithlab_cpp/smithlab_os.hpp by moving extract_region functions to GenomicRegion.hpp. amrfinder.cpp is changed correspondingly.
Added constructors, functions, and overloaded stream operators to prepare for allelicmeth update
fix the way to load old methcount results so that the sequence info is retained
Updated trackmaking section to include step to convert methcounts output to bed format for wigToBigWig
Merge branch 'master' of https://github.com/smithlabcode/methpipe
Major revisions to allelicmeth: now operates more like methcounts.
Minor formatting
Fixed command in trackbuildingsection that would produce a fileseek error due to recent bedToBigBed updates.
Merge branch 'master' of https://github.com/smithlabcode/methpipe
replace the using of function roundf with std::tr1::round
replace the using of function roundf with std::tr1::round
Changed 3 occurrences of 'LC_ALL=C;' in the manual. This is wrong and caused users asking why sort didn't work.
Added option to omit FDR cutoff application
Merge branch 'master' into dmr-merge