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MACS v2.2.6
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@taoliu taoliu released this 12 Dec 21:02
· 873 commits to master since this release
v2.2.6
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Learn about vigilant mode.

Speed up and other fixes

New Features

  1. Speed up MACS2 with some programming tricks and code cleanup.

    The filter_dup function replaces separate_dups. The later one was
    implemented for potentially putting back duplicate reads in certain
    downstream analysis. However such analysis hasn't been implemented.
    Optimize the speed of writing bedGraph files. Optimize BAM and BAMPE
    parsing with pointer casting instead of python unpack.

  2. The comment lines in the headers of BED or SAM files will be
    correctly skipped. However, MACS2 won't check comment lines in the
    middle of the file.

Bugs fixed

  1. Cutoff-analysis in callpeak command. #341

  2. Issues related to SAMParser and three ELAND Parsers are fixed. #347

Other

  1. cmdlinetest script in test/ folder has been updated to: 1. test
    cutoff-analysis with callpeak cmd; 2. output the two lines before
    and after the error or warning message during testing; 3. output only
    the first 10 lines if the difference between test result and standard
    result can be found; 4. prockreport script monitor CPU time and
    memory usage in 1 second interval, providing a bit more accuracy.

  2. Python3.5 support is removed. Now MACS2 requires Python>=3.6.

  3. In the next release, we will remove the support for ELAND and BOWTIE
    format file, since SAM/BAM and BED format are more standard and flexible.

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