andrewdavidsmith
commented
9 months ago - 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
- uniq.cpp: adding a variable to control the max buffer size which matters for some strange data sets with hundreds of thousands of reads at the same mapping location