Changing how we detect clang vs. gcc
Fixing logging options to be compatible with arg parse
fixing the group message for the Logging options under argparse, corrected comments, forced 80c line width limit on area of code I touched.
Adding little function to safely cat files
Disallow newick trees with implied roots

(i.e. branch lengths on the root node)
Causes confusion since it creates an extra node, even though it's
allowed in the newick standard
Fixes benedictpaten/cactus#5
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Test commit.
View changes to work with os x and eclipse keplar
Use clang only on macs
Removing the " -stdlib=libstdc++" from the sonLib include file, which
was apparently necessary for some versions of clang.
Fixing test that for st_system to be portable.
add absSymPath for getting absolute paths without deref symlinks
Merge branch 'development' of https://github.com/benedictpaten/sonLib into development
Make adding implied root nodes optional to fix tests
Adding "isNewer" function
Fix.
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Adding fastq functions
Fix to fastq function
Making fasta parser robust to odd whitespace, like carriage returns.