Missing documentation for compareStrings

[gevro]

Hi, Documentation of compareStrings is missing an explanation for what it does with input of: pattern="PairwiseAlignments", subject="missing"

I believe the best place to document this would be: PairwiseAlignments-class {Biostrings}

[hpages]

This is clarified in Biostrings 2.65.4. The man page for compareStrings() (?compareStrings) now says:

pattern, subject: The strings to compare. Can be of type ‘character’,
          ‘XString’, ‘XStringSet’, ‘AlignedXStringSet’, or, in the case
          of ‘pattern’, ‘PairwiseAlignments’.

          If the first argument of ‘compareStrings()’ (‘pattern’) is a
          ‘PairwiseAlignments’ object, then the second argument
          (‘subject’) must be missing. In this case ‘compareStrings(x)’
          is equivalent to ‘compareStrings(pattern(x), subject(x))’.

Biostrings 2.65.4 should become available in BioC 3.16 (devel) in the next 24-48 hours via BiocManager::install().

[gevro]

Thank you