DCC 0.5.0 released

We are happy to release the new major version 0.5.0 of DCC as of today.

Major changes:

• DCC 0.5.0 now requires Python 3.5 and will NOT work anymore with Python 2.x.

Fixes:

• DCC now correctly handles the new Chimeric.out.junction files of STAR with headers
• Fixing incorrect line number is warnings: 85df4b3 (Thanks to @buddej)

DCC 0.4.8 released

We are happy to release version 0.4.8 of DCC as of today.

Critical fixes:

• An incorrect handling of mate2 junction files has been fixed. The fix of this issues may result in a higher number of detected circRNAs if using -Pi mode / paired end data.

Updating DCC to version 0.4.8. and re-running DCC is highly recommended for those data sets.

Other fixes:

• #58 : An unspecific error message that could be produced under various circumstances has been fixed
• #66 : IOError: [Errno 2] No such file or directory: 'CircRNACount'
• #36 : BAM error

DCC 0.4.7 released

We are happy to release version 0.4.7 of DCC as of today.

Improvements:

• DCC now check list input files, i.e. samplesheet, mate1/2 and bam_files.txt for empty lines and ignores those

Fixes:

• #57: Newer numpy package versions generated a Future warning when running DCC. The code has been updated to address this warning.

DCC 0.4.6 release

Fixes:

• DCC 0.4.6 removes a redundant data column from the LinearCount output file.

DCC 0.4.5 release

We are proud to release version 0.4.5 of DCC as of today.

Improvements:

• #48: CircSkipJunctions does not contain junction orientation

Fixes:

• #25: DCC does not check if annotation file is present during start
• #26: CircCoordinate file gene annotation conatins only "." when run without -ss
• #27: DCC output directory needs to be created before logging starts
• #28: Temporary file names for circRNA counts are wrongly concatenated
• #29: Temporary file problem
• #30: fails if -R is not set
• #31: IndexError: list index out of range
• #32: Cant find 'tmp_unsortedNoChrM'
• #36: BAM error
• #38: Check for sorted BAM files fails if first chromosome has less than 100 mapped reads
• #39: Single End Read run crashes
• #40: Extract the circRNA sequences using the script getcircfasta
• #42: DCC crashes with -fg set and -M unset
• #46: Gene name annotations not included in final results
• #47: Dubious CircSkipJunctions output

Notes:

• The CircSkipJunctions output file now has a fourth default column that includes the strand of the annotation. Also, all non-zero entries have now the following format: 1:9930458-9935491-:2, therefore including the strand information before the read count.

DCC 0.4.4 release

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

DCC 0.3.4 released

Release 0.3.4. is a bug fix release solving issue #9.

The issue effected runs where no mate information was used and a newly implemented file check wrongly assumed the mate files have to be in place.

DCC 0.3.3 released

As of today, we released DCC version 0.3.3.

Changes compared to 0.3.2:

• Fixed an issue that resulted in only-0 LinearCount files
• For most input files check routines have been implemented to assure all files and directories exist during program start
• Fixed numerous typos and clarified log and error messages
• Added pandas as dependency (DCC would not check if it's installed and just crash when not installed)
• Fixed issue #6 (specific combination of -F without -D crash the program)
• Fixed issue #7 (IndexError: list index out of range during host gene counting)
• Fixed issue #2 (empty chimeric junction files crash the program)
• Fixed issue #1 (goes together with #2 )

version0.3.2

• Support for secondstrand data
• Fixed a bug for read count for paired end data. Few circles will be influenced.

Version 0.3.1c

v0.3.1c

Update circAnnotate.py