Set alternate alphabet to exclude lowercase by default #10
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Line 377: Remove first part of if condition (i.e. eliminate "(ali->alphabet == codesAA) &&" and clean outer level of brackets) Line 381: Remove condition on codesAA (i.e. always true), i.e. just the following remains: if (seq(ali->target, i) == 0) siteValid[i] = 0; Line 530: Remove condition on codesAA (i.e. always true), i.e. change line to if (c == '.') c = '-';
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This change just removes the hard coding of alphabet to be codesAA for removing lowerCase and '.' gaps.