Release 2.11

• Allow parsing converted CASAVA headers
• Include static libraries in development package

Version 2.10

• Fix buffer overrun during parsing
• Add a primer filter module
• Fix -module flag in pandaxs

Version 2.9

• Skip read pairs with no sequence
• Do not free an empty line buffer.
• Allow reading separate index reads
• Miscellaneous bug fixes

Version 2.8

• Add a plugin to display overlaps examined
• Add -D flag to add a penalty for shifting primers
• Added UPARSE algorithm
• Add FastqJoin algorithm
• Add FLASH algorithm
• Add Sitch algorithm
• Fix bug causing spurious “no sequences” with one thread
• Issue an error if the command line arguments have UTF-8 characters
• Remove min_readqscore since it doesn't work as advertised
• Sanity check sequence length after primer stripping

Version 2.7

• Supress warning about PHRED+64 when the header is CASAVA 1.7+
• Fix stack corruption causing crashes
• Add support for EBI SRA header formats
• Set the maximum overlap back to read length
• Allow restricting the maximum overlap length
• Deal with DOS formatted files gracefully
• Fix probability to PHRED conversion
• Add a program to compare differening conditions
• Fix RDP scoring algorithm

Version 2.6

• New alignment algorithms: RDP maximum likehood and PEAR
• New filters: PEAR statistical test, the bits saved in the overlap region,
  the read Q score, and the minimum PHRED quality score
• Detect compression automatically.
• Allow writing failed alignments with quality information (-U).
• Parse sequence headers from the Short Read Archive
• Make sure to preserve custom k-mer table size when threaded.
• Fix LTDL unreferencing bug where non-loaded modules would incorrectly decrement
  the LTDL reference count, causing breakage of still-loaded modules.

Version 2.5

• Add support for output and log files via Writer
• Add thread-friendly output writing system
• Added asynchronous reader to improve input read speed
• Added support for reads which overhang

• Fix memory allocation bug in when minoverlap specified by the user is
  

  greater than either of the input sequences.
• Salvage extra sequences when a minimum overlap is applied.
• Updated checkid to include CASAVA version
• Collect information about sequences that fail to assemble by hashing