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versionHistory.txt
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versionHistory.txt
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Version 0.1: Initial Release
Version 0.11: Fix: SE parameter passing
Version 0.14: Feature: Implement support for PHRED33 quality score encoding (-phred33 or -phred64)
Version 0.15: Feature: Support for logging the trimming (-trimlog <logfile>)
Version 0.17: Feature: Support for HEADCROP task (HEADCROP:<BasesToRemove>)
Version 0.20: Multithreading support
Summary trim statistics
Fix: Incorrect alignment score in ILLUMINACLIP
Version 0.22: Feature: Support ZIP and BZIP2 format
Feature: Basic support for short adapters in simple mode in ILLUMINACLIP
Version 0.24: Fix: Handle concatenated gzip files
Version 0.25: Feature: Support for -jar invocation. The ‘old’ method, using the explicit class, continues to work
Fix: Ensure input files are read only once, to allow streaming via shell
Fix: Report failures correctly in multi-threaded mode
Version 0.27: Feature: Add support for ‘keep reverse’ and ‘minimum adapter length’ to palindrome mode in ILLUMINACLIP
Feature: Support for short adapters and/or short overlaps
Feature: Add MAXINFO trimmer
Performance: Improve FastQ parser and serializer
Version 0.30: Feature: Add AVGQUAL trimmer
Fix: Correct ‘half-window’ clipping from end of reads in SLIDINGWINDOW (bug introduced in 0.27)
Performance: Various improvements to simple alignment in ILLUMINACLIP
Internal: Clean up & refactor ILLUMINACLIP implementation
Version 0.32: Feature: Automatic detection of PHRED encoding
Feature: Automatic setting of threads based on cpu cores (up to 16)
Feature: Support for template-based input and output file names
Fix: Add missing MANIFEST.MF file
Version 0.33: Fix: Tolerate wider range of QUAL values in automatic PHRED detection
Version 0.35: Feature: Only use automatic thread setting with <=8 cores, up to a maximum of 4 threads
Feature: Add read pairing validator
Feature: Improved parameter handling and problem detection
Feature: Added 'quiet' mode for log messages
Fix: Better error handling in parser
Fix: Tolerate different length input files in paired mode
Performance: Improve trimming using different sensitivity based on adapter length
Version 0.36: Feature: More flexible HEADCROP trimmer options
Feature: TAILCROP trimmer
Feature: Show version
Fix: Concatenated gzip files
Version 0.38: Feature: Stats summary file
Feature: BASECOUNT trimmer
Version 0.39: Feature: More flexible HEADCROP/TAILCROP trimmer options
Version 0.40: Feature: Parallel GZIP/BZIP2 compression