Difference between revisions of "C++ Library: general Change Log"

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= libcsg Change Log =
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{| style="width:100%; background:#FF8989; margin-top:1.2em; border:1px solid #ccc;" |
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<div style="font-size:162%; border:none; margin:0; padding:.1em; color:#000;">This change log & the statgen repository have been DEPRECATED
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To see changes for the new libStatGen repository, consult the github history:
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https://github.com/statgen/libStatGen/commits/master/</div>
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|}
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= general 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.  
 
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 ==
 
== Enhancements/Updates/Fixes ==
 +
=== 11/01/2010 ===
 +
* made part of statgen library
 +
 +
=== 09/29/2010 ===
 +
* Updated CigarRoller to have a method to set a CigarRoller from another CigarRoller.
 +
* Cigar: Add static methods to return whether or not an operation is a clip (isClip) or indicates bases found in the query sequence (foundInQuery).
 +
* Update how to specify stdin file type - now use the ifileCompression parameter to ifopen.
 +
 +
=== 09/24/2010 ===
 +
* Add capability to read/write from/to stdin/stdout
 +
** Updated most cout/stdout to cerr/stderr for info/error messages.
 +
* Added a BaseUtilities Class for determining information about bases & qualities.
 +
 +
=== 09/15/2010 ===
 +
* Fix bug in BgzfFileType.  For BGZF - EOF is determined when 0 bytes read, but if 0 were specified to be read, it is not EOF.
 +
 +
=== 08/24/2010 ===
 +
* Paul updated Cigar to have a getCigarString that takes std::string instead of just String.
 +
 +
=== 08/12/2010 ===
 +
* Fix bug in Cigar::getQueryIndex from reference position that did not first check if the query and reference maps were created.
 +
 +
=== 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 [[C++ Class: InputFile|'''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 <code>void InputFile::setWriteFileType(FileTypeEnum fileType)</code> 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 ===
 
=== 5/20/2010 ===
 
* Update [[C++ Class: InputFile|'''InputFile''']]
 
* Update [[C++ Class: InputFile|'''InputFile''']]

Latest revision as of 12:57, 1 May 2012

This change log & the statgen repository have been DEPRECATED

To see changes for the new libStatGen repository, consult the github history:

https://github.com/statgen/libStatGen/commits/master/

general 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

11/01/2010

  • made part of statgen library

09/29/2010

  • Updated CigarRoller to have a method to set a CigarRoller from another CigarRoller.
  • Cigar: Add static methods to return whether or not an operation is a clip (isClip) or indicates bases found in the query sequence (foundInQuery).
  • Update how to specify stdin file type - now use the ifileCompression parameter to ifopen.

09/24/2010

  • Add capability to read/write from/to stdin/stdout
    • Updated most cout/stdout to cerr/stderr for info/error messages.
  • Added a BaseUtilities Class for determining information about bases & qualities.

09/15/2010

  • Fix bug in BgzfFileType. For BGZF - EOF is determined when 0 bytes read, but if 0 were specified to be read, it is not EOF.

08/24/2010

  • Paul updated Cigar to have a getCigarString that takes std::string instead of just String.

08/12/2010

  • Fix bug in Cigar::getQueryIndex from reference position that did not first check if the query and reference maps were created.

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.


Known Issues

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