Re: [Seqan-dev] Zlib linking errors under 64bit Windows 7

[Theodore Omtzigt <theo@stillwater-sc.com>]

I have got the linking to work outside of the SeqAn CMake build environment, so I have now at least isolated it to be a problem in the SeqAn build environment.

However, I also run into a format error on a fastq file that is passing with the standard code from Genome Research Lab (kseq.h).

The problem occurs in the last test in this code fragment from read_fasta_fastq.h
template <typename TIdString,
          typename TQualString,
          typename TFile,
          typename TPass>
inline int
_readQualityBlock(TQualString & qual,
                  RecordReader<TFile, TPass > & reader,
                  unsigned const seqLength,
                  TIdString const & meta,
                  Fastq const & /*tag*/)
{
    // READ AND CHECK QUALITIES' META
    if (atEnd(reader))
        return EOF_BEFORE_SUCCESS;
    if (value(reader) != '+')
        return RecordReader<TFile, TPass >::INVALID_FORMAT;
    goNext(reader);
    if (resultCode(reader))
        return resultCode(reader);
    if (atEnd(reader)) // empty ID, no sequence, this is legal? TODO
        return 0;

    CharString qualmeta_buffer;
    int res = readLine(qualmeta_buffer, reader);
    if (res && res == EOF_BEFORE_SUCCESS)
        return EOF_BEFORE_SUCCESS;
    else if (res)
        return RecordReader<TFile, TPass >::INVALID_FORMAT;

    // meta string has to be empty or identical to sequence's meta
    if ((qualmeta_buffer != "") && (qualmeta_buffer != meta))
        return RecordReader<TFile, TPass >::INVALID_FORMAT;
...

and the test fails because of the qualmeta_buffer not being equal to meta.
+    meta    {data_begin=0x001757e0 "EAS18:1:1:1:1:1119:0/1ÍÍÍÍÍÍÍÍÍÍÍÍÍÍýýýý««««««««" data_end=0x001757f6 "ÍÍÍÍÍÍÍÍÍÍÍÍÍÍýýýý««««««««" data_capacity=32 }    const seqan::String<char,seqan::Alloc<void> > &
+    qualmeta_buffer    {data_begin=0x0017dc40 "EAS18:1:1:1:1:1119:0/1 ltrim=1 rtrim=38ÍÍÍÍÍÍÍÍÍÍÍÍÍÍýýýý««««««««þîþîþîþ" data_end=0x0017dc67 "ÍÍÍÍÍÍÍÍÍÍÍÍÍÍýýýý««««««««þîþîþîþ" data_capacity=49 }    seqan::String<char,seqan::Alloc<void> >

that section: " ltrim=1 rtrim=38" appears to be a format difference that kseq.h accepts as a valid quality segment, but read_fasta_fastq.h does not.

So, this question now has bifurcated into a second question and that is what is considered a valid fastq format?