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CHANGES.txt
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CHANGES.txt
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Open Genomics Engine
Version 0.4 - 31 January 2013
* Removed dependency on BamTools for some internal components
* Rewritten BAM BGZF code increases performance
* Reduced memory consumption of many functions
* Increased performance on machines with a small number of cores (<4)
* Increased performance of MarkDuplicates
* Fixed small bugs affecting stability and correctness that were found through automated testing
* Other bug fixes
Version 0.3 - 31 October 2012
* New multithreaded IO subsystem increases IO performance. Replaces bamtools-based IO.
* Add repeatseq function for micro satellite detection. Implements repeatseq algorithm from original repeatseq program (https://github.com/adaptivegenome/repeatseq), with additional parallelization.
* Add experimental execute function for execution of workflow scripts. Scripts describe a pipeline of commands to be run in serial or parallel, and checks to ensure that commands have run successfully. See the command reference documentation for more details.
* Internal refactoring has improved performance of many command read/write operations
* Remove most internal dependence on BamTools
* Statistics command can now check if a file is properly sorted
* The compare function can now use SAM files as input
* Many other minor improvements
* Other bug fixes
Version 0.2 - 30 August 2012
* Add localrealignment function to realign reads around known indels. Output is comparable to GATK's IndelRealigner, but execution may be up to 12x faster on some hardware.
* Add compare function for comparing similar BAM files
* Add history command for reviewing the list of commands used to generate a file (using @PG records)
* Add more information (version number, unique IDs) to @PG records to enhance traceability
* Generate indexes for FASTA files when they aren't present
* Greatly reduce memory usage of the coverage command when using the --binsize option
* Add ability to detect truncated and corrupt BAM files in many cases
* The mark duplicates and mergesort option for deleting duplicate reads has been moved to -D from -d
* Fix issue that caused some BAM files generated by OpenGE to be incompatible with other tools. These files can be fixed by running the file through the view with no arguments (e.g. "openge view in.bam -o out.bam").
* Fix bug preventing streaming in BAM files
* Fix several small issues with SAM format reading and writing
* Other bug fixes
Version 0.1.2 - 20 July 2012
* Add 'coverage' command, allowing analysis of coverage of a genome
* Improve SAM I/O speed, and fix several errors in parsing and generating SAM files
* Add ability to filter by read length, by minimum quality
* Add FASTQ output support
* Add ability to trim reads when generating a FASTQ file
* Add testing support to the codebase (CTest, see developer docs)
* Add @PG records to SAM and BAM files, containing the command line options used to generate the file
* Other bug fixes
Version 0.1.1 - 16 June 2012
* Split by chromosome when marking duplicates
* Multithreaded sorting when marking duplicates
* Fixed --tmpdir parameter being ignored
* Added SAM output support (experimental)
* Added distribution of read lengths to statistics command
* Removed convert command
* Other bug fixes
Version 0.1 - 2 June 2012
* Initial release