2012-04-06: mrFAST version 2.1.0.6 release:

• Support for read length up to 1000 bp.
• Edit distance now defaults to 4% of the read length, and can still be changed through the -e parameter.
  
• Bug that caused a slight reduction in sensitivity is fixed.
• The batch mode (-b) is deprecated. Input the reference as multi-sequence FASTA file only.
  

2012-03-07: mrFAST version 2.1.0.5 release:

• Automatic detection of FASTQ quality offset. mrFAST now rescales quality offset to 33 (Sanger format) if the input offset is 64.
• --maxdis parameter now defaults to 300, and --maxoea defaults to 100. To disable, pass --maxdis 0 and/or --maxoea 0.
• In paired end mode, best concordant and best discordant mapping files are merged into a single SAM file.
• Bug fixes in the CIGAR string generation in paired end mode.
• --discordant-vh option is now selected by default in paired end mode.
  

2012-02-21: mrFAST version 2.1.0.4 release:

• Better memory management in paired-end mode.
• Sample set is added (genome file, sequence files, command line and expected output).
  

2011-12-15: mrFAST version 2.1.0.3 release:

• Segmentation fault when main memory is unsufficient is fixed.
  

2011-12-03: mrFAST version 2.1.0.2 release:

• Bug in parsing parameters is fixed (bug #3436724).
• Unused memory allocations cleaned.
  

2011-11-07: mrFAST version 2.1.0.1 release:

• Segmentation fault when CIGAR string is too large is fixed (long sequences, with high edit distance).
• Several typos in error messages are fixed.
• Program crash when incorrect parameters are entered is fixed.
• If the length of the pairs of reads in paired-end mode are different, mrFAST now trims the longer end to match the shorter end sequence.
• Compilation warnings with some versions of gcc are cleaned.
  

2011-09-12: mrFAST version 2.1.0.0 release:

• Several bugs are fixed.
• New parameter --maxoea now limits the maximum number of  locations for one end anchored (OEA) sequences. This will help substantially reduce the output file size. For NovelSeq use, we recommend to set this parameter to at least 100.
• New parameter --maxdis now limits the maximum number of  locations for discordant read pairs in the DIVET file. This will help substantially reduce the output file size. For VariationHunter use, we recommend to set this parameter to at least 300.
  

2010-09-26: mrFAST version 2.0.0.5 release:

• Several minor bugs are fixed.
  
• Sequence and quality information of the unmapped ends of OEA pairs are added to the SAM-compatible OEA output file for NovelSeq. Next release of NovelSeq will be able to parse this file. Please contact NovelSeq authors if you need help with format conversion in the mean time.
• User manual uploaded.
  

2010-08-26: mrFAST version 2.0.0.3 release:

• One end anchored (OEA) map locations for novel sequence insertion detection with NovelSeq added. The output format is SAM, please contact NovelSeq authors if you need help with format conversion.
  

2010-07-24: mrFAST version 2.0.0.2 release:

• Minor bug in VariationHunter output (--discordant-vh) in reporting probability score is fixed.

2010-06-30: mrFAST version 2.0.0.1 release:

• Minor bug in VariationHunter output (--discordant-vh) is fixed.

2010-06-21: mrFAST version 2.0.0 release:

• New semi-cache-oblivious algorithm to improve mapping speed.
  
• Longer reads and more indels are supported.
• Improved user interface similar to mrsFAST.
• SAM format output.