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dnmtools
Tools for analyzing DNA methylation data
https://dnmtools.readthedocs.io
GNU General Public License v3.0
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xcounts header
#202
Closed
andrewdavidsmith
closed
10 months ago
andrewdavidsmith
commented
10 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