[Seqan-dev] ESA computation

[Robert Bakaric <bakaric@evolbio.mpg.de>]

Hi,

I have a very basic question and it relates to constructing suffix 
arrays. I know that i can construct and an SA by invoking : 
createSuffixArray(); function and if i want  a specific algorithm i do 
this :

createSuffixArray(SA, seq, BwtWalk<BwtWalkFast>());

Now, when i want to compute LCP i saw this example:

indexRequire(myIndex, EsaLcp());

How do i specify that my SA in this case should be created with the same 
BWT algorithm as in the case above.

concrete example:
:

    seqan::String<char, seqan::MMap<> > mmapString;
    if (!open(mmapString, toCString(options.inputFileName), 
seqan::OPEN_RDONLY))
        return 1;  // Could not open file.

    // Create RecordReader.
    seqan::RecordReader<seqan::String<char, seqan::MMap<> >,
                        seqan::DoublePass<seqan::Mapped> > 
reader(mmapString);

    // Read file in one pass.
    seqan::StringSet<seqan::CharString> ids;
    seqan::StringSet<seqan::CharString> seqs;
    if (read2(ids, seqs, reader, Fasta()) != 0)
        return 1;  // Could not read file.

    typedef Index< StringSet<String<char> > > TMyIndex;
    TMyIndex myIndex(seqs);

    indexRequire(myIndex, EsaLcp());

:

Thank you