Bio-SAGE-DataProcessing
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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.
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