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DCC 0.4.4 release
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@tjakobi tjakobi released this 10 Aug 08:54
· 64 commits to master since this release
v0.4.4
087e25b

We are proud to release the first new major version of DCC, version 0.4.4 as of today.

The new 0.4 branch contains major rework compared to the now legacy 0.3 branch.

Improvments:

  • Removed pybedtools dependency: Due to some problems with pybedtools implementations DCC now uses own routines for several tasks
  • Multithreading: DCC now is able to use multiple CPU cores, e.g. by using -T 4 uses 4 cores during host gene counting and circRNA detection
  • User-specified output and temporary directories: By using -O /path/ the output directory can be specified, while -t /tmp_path specifies the temporary directory
  • Improved documentation: The documentation was improved and streamlined to better assist first-time users
  • BAM file check: Supplied BAM files are now checked for sorting during program start; the user is notified if files are unsorted
  • Python dependencies: The setup now correctly checks for up-to-date versions of the required packages

Fixes:

  • Fixed #10: CircCoordinates has not column labels anymore
  • Fixed #11: Problem with temporary file handling during mpileup
  • Fixed #12: Annotation in develop branch produces different results
  • Fixed #13: Deletion of CircSkip temp files crashes if no CircSkip files present
  • Fixed #14: DCC log file does not report the command line anymore
  • Fixed #16: Allow user to specify output location of DCC generated files
  • Fixed #17: Allow user to specify temporary location of DCC generated files
  • Fixed #19: Check if input BAM files are sorted by coordinate
  • Fixed #20: convertjunctionfile2bamfile() fails if BAM files are not named in STAR fashion
  • Fixed #21: Check functions of the CircSkip routines
  • Fixed #22: -temp / -k option: file cleanup does not work and fails for some files
  • Fixed #23: SJ.out.tab and BAM file requirements are not part of the documentation
  • Fixed #24: Linear count files only contain zero values and no actual counts

Notes:

  • The -temp flag of the legacy 0.3 version used to keep temporary files was replaced by -k in the 0.4 release
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