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Author: jmduarteg
Date: Fri Nov 16 10:02:32 2012 UTC (9 years, 6 months ago)
Log Message:
Fixed important issues with searching and alignment of homologs: 
- ids and coverage were calculated wrongly, based on all BlastHsps for a hit. Now based on single Hsps
- fixed bug in BlastHsp.getQueryCoverage: was miscalculating the coverage by 1 unit
- the useHspsOnly parameter in alignment didn't make much sense. We need always to use the hsp segments only, extending to the full sequence is dangerous and in any case does not make sense at all if the clustering is done in hsps only

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