Permalink
Commits on May 5, 2017
  1. Update callpeak_cmd.py

    committed on GitHub May 5, 2017
  2. Update PeakDetect.pyx

    committed on GitHub May 5, 2017
  3. Update README.rst

    committed on GitHub May 5, 2017
  4. Update PairedEndTrack.pyx

    Related to #189
    committed on GitHub May 5, 2017
Commits on Mar 22, 2017
  1. Update PeakDetect.pyx

    Suggested by #173
    committed on GitHub Mar 22, 2017
Commits on Sep 20, 2016
  1. Merge pull request #149 from shengqh/master

    fix righ_pos to right_pos (by shengqh)
    committed on GitHub Sep 20, 2016
Commits on Sep 12, 2016
  1. fix righ_pos to right_pos

    shengqh committed on GitHub Sep 12, 2016
Commits on May 19, 2016
  1. Related to issue #122. Check ndarray size, then resize it to half size

    if the half size is less than 10K.
    committed May 19, 2016
Commits on May 16, 2016
  1. Merge pull request #129 from mr-c/spelling2

    more spelling tweaks :-)
    committed May 16, 2016
Commits on May 13, 2016
  1. more spelling tweaks :-)

    mr-c committed May 13, 2016
Commits on Mar 9, 2016
  1. Merge branch 'master' of https://github.com/taoliu/MACS

    # 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.
    committed Mar 9, 2016
  2. Remove filtering criteria of bwflag&2048 so PCR/Optical duplicate will

    still be read. Update changelog.
    committed Mar 9, 2016
Commits on Mar 5, 2016
  1. Merge pull request #120 from mr-c/spelling-fixes

    Fix spelling. From @mr-c
    committed Mar 5, 2016
  2. Fix spelling

    mr-c committed Mar 5, 2016
Commits on Feb 26, 2016
  1. Release 2.1.1.

    committed Feb 26, 2016
  2. Fix the issue: #108 when no peaks in a chromosome, PeakIO

    get_data_from_chrom will throw an error. Thank @kannan-kasthuri!
    committed Feb 26, 2016
Commits on Feb 15, 2016
  1. Fixed a bug so that in PE mode after filtering duplicates, the first …

    …read
    
    pair of a chromosome won't be incorrectly skipped.
    committed Feb 15, 2016
  2. A more flexible format, BEDPE, is supported. Related to issue

    #112. Clean up the codes -- remove PYSAM support. Fix the calculation
    of average fragment length for PE mode. Now whether 'PE mode' is on or
    off will be recorded in the output files.
    committed Feb 15, 2016
Commits on Feb 12, 2016
Commits on Jan 30, 2016
  1. Replace C FLAG '-Ofast' with more compatible '-O3 -ffast-math' in

    setup.py and setup_w_cython.py. Related to #71, #91, #109.
    committed Jan 30, 2016
Commits on Dec 23, 2015
  1. Merge pull request #97 from daler/master

    add option to specify tempdir from command line. Related to #105.
    committed Dec 23, 2015
Commits on Dec 22, 2015
  1. One more line in ChangeLog.

    committed Dec 22, 2015
  2. Fix a bug related to the broad peak calling function in previous

    versions. The gaps were miscalculated, so segmented weak broad calls
    may be reported, and sometimes you would see peaks with lower than
    cutoff values in the output files.
    
    "Potentially" Fixed issue #105 on temporary files, need further followup.
    committed Dec 22, 2015
Commits on Oct 9, 2015
  1. Update FixWidthTrack.pyx

    Fix a bug while dealing with some chromosome only contains one read (pair). The size of dup_plus/dup_minus arrays after filtering dups should +1.
    committed Oct 9, 2015
  2. Update PairedEndTrack.pyx

    Fix a bug while dealing with some chromosome only contains one read (pair). The size of new_locs after filtering dups should +1.
    committed Oct 9, 2015
Commits on Sep 16, 2015
Commits on Jul 31, 2015
  1. Update version tag.

    committed Jul 31, 2015
  2. Update ChangeLog

    committed Jul 31, 2015
Commits on Jul 30, 2015
  1. Fixed bug #86. A wrong usage of 'ndarray' caused 'callpeak --nolambda'

    hangs forever. Fixed by editting 'ndarray' -> 'array'.
    committed Jul 30, 2015
Commits on Jul 28, 2015
  1. Update README.rst

    Fixed -m description for issue #89
    committed Jul 28, 2015
  2. ChangeLog updated

    committed Jul 28, 2015
Commits on Jul 27, 2015