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biointec / brownie

Brownie
GNU General Public License v2.0
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To display number of changes in stage 5 in terms of substitutions... #8

Closed mahdiheydari closed 8 years ago

mahdiheydari commented 8 years ago

This modifications enables Brownie to display number of changes in the entire data set to correct the reads. Indels are ignored and only substitutions took into consideration. It also shows percentages of reads which have been corrected and the number of reads which are corrected by EssaMEM.

jfostier commented 8 years ago

1) Packed four parameters into a single class AlignmentMetrics. This greatly facilitates adding other metrics later on and prevents an explosion of performance counters in the other alignment classes 2) findByMEM was always false. This is fixed. 3) The number of substitutions was incorrectly computed. The correct formula is (read.length() - score)/2 because per subsitution, the score drops by 2 points (1 (match) -> -1 (mismatch)).

Please revise.