Revision history for Bio-Trace-ABIF 0.01 2006-10-26/17:30 First version, released on an unsuspecting world. 0.02 2006-11-15/22:30 Added method to compute CRL (Contiguous Read Length). A few bugs fixed in the documentation. 1.00 2007-02-16/12:30 - Added methods to read all the ab1 file tags specified by the ABIF format, including fsa tags. - Added method write_tag() to overwrite existing data. - Methods returning a scalar now return 'undef' in case of error (e.g., tags not found). - Signed shorts and longs are correctly unpacked. - Methods sorted alphabetically. - Fixed a version mismatch. - contiguous_read_length() has now mandatory arguments. Trimming the ends is now optional. The method returns (-1, -1) when no CRL exists. - Fized a bug in sample_score() occasionally causing division by zero. Also, sample_score() in some cases returned negative values: this has been fixed, too. - Changed the semantics of clear_range_start() and clear_range_stop(): both methods return -1 if no clear range exists. - Fixed bugs in clear_range_start() and clear_range_stop() that would cause an error in some (very unfortunate) cases. - Added clear_range() method, which returns an interval (start, stop). - Much faster conversion from binary to floats. - Fixed a bug in analysis_protocol_xml(). 1.01 2007-04-03/18:05 - Fixed bug causing wrong return values from analyzed_data_for_channel() and raw_data_for_channel() methods. 1.02 2008-12-17/18:42 - Fixed a bug in order_base(), raw_trace() and trace() methods. WARNING! Note that the semantics of order_base() has changed! Now, the method returns the channel number, not the array index (to avoid off-by-one errors when using this method with other methods requiring a channel as a parameter). - Fixed a bug in offscale_peaks(). - Added a channel() method, returning the channel number corresponding to a given base. - Slightly improved documentation. 1.03 2010-01-13/18:58 - open_abif() returns 0 when it opens a file whose directory index is corrupted, instead of producing lots of error messages (bug reported by Malcolm Cook). - Added method peaks() to get the detected peaks from the sample results window in GeneScan (including size, peak height, and peak area). Kindly provided by Jason Gilder (and by one of his students!) - Method module_version() is now public. 1.04 2010-01-13/19:49 - Fixed copyright notice in ABIF.pm.