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This release has the following new improvements:
- Bugfix for "preprocess mode" concurrency sorting
- Default temp file directory changed: now the current directory is your default temp file directory unless you use the "-p" option
- Slight performance increase
This release provides a major bug-fix for smaller datasets. If the dataset contained fewer than 10,000 discordant reads, the sort algorithm would fail due to a lack of information.
- RAPTR-SV preprocess mode now supports variable length read BAM files by selecting the most common read length as a standard for read filtering/trimming
- preprocess mode also allows the user to designate the optimal read length size (if he/she is unsatisfied with the automatic detection) with the "-l" command line argument
- Fixed bugs with logger statements
- Fixed the bug that prevented the program from deleting the temporary MrsFAST SAM file
This release has some minor improvements over the previous versions, including several bug fixes.
- Better logging
- Better threading potential
- Bug fixes
Improvements from initial release:
- minor bug fixes
- improvements to weight cover algorithm to increase threading
- dynamic programming set recalculation
- discordant read output file format change
- improvements to preprocessing algorithm
This is a version of RAPTR-SV that is compatible with JDK version 1.7 and upwards. Better performance (and threading) is achieved with the use of the JDK1.8 RAPTR-SV; however, this release will allow the use of other Java programs that are only compatible with JDK1.7.