C++ Library: general Change Log

libcsg Change Log

This page tracks the updates/enhancements that have been updated in the git repository. It is primarily used to track the user interface changes, so users can see what bugs have been fixed, or what new features have been added.

Enhancements/Updates/Fixes

08/11/2010

• Split CigarRoller into a base class, Cigar, and a child class, CigarRoller.
  • Cigar has no accessors that allow modification to the cigar, but it does allow for modification to the class due to lazy evaluation.
  • CigarRoller is the child class that allows modification of the cigar.

08/03/2010

• Add methods to CigarRoller
  • getNumOverlaps - takes a region and the query start position and returns the number of overlaps (cigar 'M') in that region
  • getRefPosition - takes a query index and the query start position and returns the associated reference position or INDEX_NA
  • getQueryIndex - takes a reference position and the query start position and returns the associated query index or INDEX_NA

07/16/2010

• Cigar Roller: fix the way soft clips are interpreted for mapping between the reference and the read indices. They were being treated as if they did not exist in neither the reference nor the read. They are now treated like inserts, in the read, but not in the Reference.

6/23/2010

• Update InputFile
  • Renamed GzFileType and the GZ enum to GzipFileType and GZIP enum.
  • Renamed StdFileType and the STD enum to UncompressedFileType and UNCOMPRESSED enum
  • Changed the FileTypeEnum to ifileCompression.
  • Add an ifileCompression write mode as a parameter to ifopen (and the InputFile constructor called by ifopen) that indicates the type of compression to use when opening a file for writing.
  • Modified the meaning of the DEFAULT file type when opening for write to be UNCOMPRESSED unless the filename ends in ".gz" then it is opened as GZIP.
  • Removed static method void InputFile::setWriteFileType(FileTypeEnum fileType) that allows a user to specify what type of file to open for writing rather than using the extension (default). Must be called prior to ifopen.

5/20/2010

• Update InputFile
  • Switched glf files opened for write to be opened for writing bgzf format rather than gz format.
  • Added static method void InputFile::setWriteFileType(FileTypeEnum fileType) that allows a user to specify what type of file to open for writing rather than using the extension (default). Must be called prior to ifopen.

5/13/2010

• Update CigarRoller
  • added handling of operation "N" with enum value skip.
  • added getQueryIndex and getRefOffset to map between a query index and reference offset based on the cigar string.
  • Renamed getMatchCount to getExpectedQueryBaseCount so the name better described its function.
  • Moved the cigarOperations vector to private.

5/3/2010

• Updated BGZF Files to check for the empty BGZF block at the end when being opened. The open fails if the block is not there unless the static method to not require it is called: BgzfFileType::setRequireEofBlock(false);

4/5/2010

• Modified IFILE class methods ifread & readFromFile to return an int rather than unsigned int. This aligns with the return values of gzread & fread.
• Modified the FileType classes method read to return int rather than unsigned int. This aligns with the return values of gzread & fread.
• Modified the String::ReadLine to return an int status rather than a String& to the class. A return value <= to 0 is an error. A positive return value is success.
• Modified FastQFile.cpp, lanecheck.cpp, StringHash.cpp to reflect the updated ReadLine return value.