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Published December 12, 2019 | Version v2.2.6
Software Open

taoliu/MACS: MACS v2.2.6

Authors/Creators

  • 1. Roswell Park Comprehensive Cancer Center
  • 2. Radboud University
  • 3. University of Freiburg
  • 4. @common-workflow-language
  • 5. Macquarie University
  • 6. National Institutes of Health (NIH), National Institute of Child Health and Human Development (NICHD)
  • 7. University of Colorado School of Medicine
  • 8. @aertslab
  • 9. Duke University

Description

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.

Files

taoliu/MACS-v2.2.6.zip

Files (133.8 MB)

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md5:0f74b3f88fa4cb56ef91bbae0f44744c
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Additional details

Related works

Is supplement to
https://github.com/taoliu/MACS/tree/v2.2.6 (URL)