Bio-SAGE-DataProcessing

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lib/Bio/SAGE/DataProcessing.pm  view on Meta::CPAN


  1.20 2004.10.15 - Minor spelling errors and misuse of terminology fixed in docs.
                  - Module now allows FASTA files with a blank line folling the
                    header (denoting an attempted read with no sequence), but prints
                    a warning to STDERR that this has happened. Module died previously.
  1.11 2004.06.20 - Added flag in constructor to keep duplicate ditags.
  1.10 2004.06.02 - Wrote new documentation and modified several methods to use the read-by-read
                    processing approach (see line below).
                  - Revamped the module to conserve memory. Reads are now processed one at a time
                    and then discarded. The memory requirements in the previous versions were
                    prohibitive to those with regular desktop machines.
                  - The Bio::SAGE::DataProcessing::Filter package can be subclassed to create
                    custom filters at the ditag and tag processing steps (previous versions only
                    allowed one approach to ditag/tag filtering).
  1.01 2004.05.27 - Fixed bug where extract_tag_counts didn't work with quality cutoff defined.
                  - extract_tags was not applying the get_quality_cutoff value (was returning all data)
                  - Duplicate ditags are now removed by default.
  1.00 2004.05.23 - Initial release.

=cut



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