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Commits on Apr 20, 2015
  1. 2015.4.20 release

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  2. Fix bug in pileup_a_chromosome function of PairedEndTrack. Shouldn't

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    pass partial numpy array to quick_pileup since that will mess up with pointers.
Commits on Apr 6, 2015
  1. Update README.rst

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Commits on Mar 17, 2015
  1. Merge branch 'master' of https://github.com/taoliu/MACS

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    # Please enter a commit message to explain why this merge is necessary,
    # especially if it merges an updated upstream into a topic branch.
    #
    # Lines starting with '#' will be ignored, and an empty message aborts
    # the commit.
Commits on Mar 13, 2015
  1. Update ChangeLog

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    Update ChangeLog (Not finished)
  2. Update ChangeLog (not finished)

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  3. Merge pull request #71 from aertslab/fix_file_descriptor_leak

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    Close file descriptors for temporary files after creating them with mkstemp(). -- by ghuls
Commits on Mar 12, 2015
  1. @ghuls

    Close file descriptors for temporary files after creating them with m…

    ghuls authored
    …kstemp().
    
    Close file descriptors for temporary files after creating them with mkstemp()
    to avoid leaking file descriptors and running out of file descriptors or
    hitting the limit or the number of file descriptors that you are allowed to
    open, which can happen when you have a lot of chromosomes or scaffolds in
    your input files.
  2. O3 -> Ofast

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Commits on Mar 10, 2015
  1. Rename source files: 1) cXXX.pyx files have been renamed as XXX.pyx;

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    2) pure C code files have first letter as 'c', such as
    cPosValCalculation.c/h/pxd; 3) subcommand files have been renamed as
    xxx_cmd.py such as callpeak_cmd.py.
    
    Optimization: now use pointer type to travel through the numpy
    arrays. Speed up to use about 1/2 time for pileup/p-value calculation
    and peak calling.
Commits on Jan 21, 2015
  1. Change version number.

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  2. Merge branch 'master' of https://github.com/taoliu/MACS

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    # Please enter a commit message to explain why this merge is necessary,
    # especially if it merges an updated upstream into a topic branch.
    #
    # Lines starting with '#' will be ignored, and an empty message aborts
    # the commit.
  3. Hide diffpeak module; While reading BAM/SAM file, filter those lines

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    with flag 0x100 (secondary alignment) or with flag
    0x800 (supplementary alignment).
Commits on Dec 18, 2014
  1. Merge pull request #62 from jayhesselberth/master

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    Thank you! It has been merged to MACS2.
Commits on Dec 1, 2014
  1. @jayhesselberth
Commits on Nov 2, 2014
  1. A bug is fixed. 'quick_pileup' needs both ends sorted, so I have to

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    sort right ends of BAMPE before passing values to it.
Commits on Oct 29, 2014
  1. Fixed bugs related to BAMPE.

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  2. Change subversion tag 20141030.

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  3. Fixed issue #53: Use SAM/BAM CIGAR to find the 5' end of read mapped

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    to minus strand. Note, this issue doesn't affect BAMPE module.
Commits on Oct 28, 2014
  1. Fixed issue #56: An incorrect sorting method had been used for PE

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    data, that will cause incorrect filtering of duplicated pairs and mess
    up coordinations.
Commits on Oct 23, 2014
  1. Related to issue #33. Explain that MACS2 will discard those SAM/BAM

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    alignments with bit 1024 no matter how --keep-dup is set.
  2. Fixed issue #51. Set GCC flags to suppress all warning and set

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    optimization flag to -Ofast.
Commits on Oct 21, 2014
  1. Revert: issue #57 seems to be related to an older version 2.0.10. The

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    previous change is unneccessary so I reverted it -- but still fixed a typo.
  2. Typo

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  3. a typo...

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  4. Fixed issue #57: chromosomes in BAM header but without any

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    alignments. Also updates on optimal cutoff calculation.
Commits on Sep 2, 2014
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