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compress counts #200
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compress counts #200
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andrewdavidsmith
commented
Dec 8, 2023
- methcounts.cpp: adding option to include a header in the counts output
- covered.cpp: minor fix in output when no args given
- symmetric-cpgs.cpp: added a function to print any header if it exists, which involves just printing leading lines that begin with # symbol
- bam_record_utils.hpp: added a function to get the target length from the header without specifying the internal header inside the bam_header object
- MSite.hpp and MSite.cpp: added a constructor from a char array with length. Also moved the logic of parsing strings to construct MSite into an initialize function which allows the same thing to be done without constructing a new object
- xcounts.cpp: adding this file to compress the counts files as small as possible
- dnmtools.cpp: adding the xcounts command
- Makefile.am: adding the xcounts.cpp file to the sources
- unxcounts.cpp: adding a tool to convert back from the xcounts format
- Makefile.am and dnmtools.cpp: adding the unxcounts command
- recovered.cpp: using getline then initalize the sites so that skipping the header is easier
- xcounts.cpp: removing output of chromosomes to stderr each time they change, not forcing a null char after the part of the buffer to be written, and making the buffer at most 128 bytes
- unxcounts.cpp: major changes for speed
…, which involves just printing leading lines that begin with # symbol
…the header without specifying the internal header inside the bam_header object
…ength. Also moved the logic of parsing strings to construct MSite into an initialize function which allows the same thing to be done without constructing a new object
…g the header is easier
…change, not forcing a null char after the part of the buffer to be written, and making the buffer at most 128 bytes
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