xcounts header

[andrewdavidsmith]

• xcounts: adding code to get a header from a fasta reference genome file
• xcounts: testing some threading issues
• several source files: checking that input file is BGZF format before using the threadpool for decompression
• bamxx submodule update
• xcounts: fixing a bug from previous commit
• unxcounts: including logic to verify header against chromosomes sequences currently just using length
• unxcounts: adding logic to only generate the counts for covered sites
• xcounts: ignoring the mutation mark on sites
• unxcounts: better error message on inconsistent header
• unxcounts: trying to find the best header termination
• unxcounts: better handling of header
• xcounts and counts: header no longer ends with end_header and also there is no space after the # in header lines
• unxcounts: fixing backwards condition for requiring coverage
• unxcounts: adding a missed spot to check for required coverage
• counts_header.cpp counts_header.hpp Makefile.am: adding counts_header stuff
• MSite.cpp: adding a loop to pass the header when trying to determine if a file is a counts file
• hmr.cpp and pmd.cpp: adding code to skip the header when reading sites
• methcounts.cpp: refactoring to move the header code into counts_header.chpp
• recovered.cpp: refactoring to move the header stuff into counts_header
• smmetric-cpgs.cpp: refactoring to move the header stuff into counts_header
• xcounts.cpp: refactoring to move the header stuff into counts_header
• unxcounts.cpp: refactoring to move the header stuff into counts_header