Re: [Seqan-dev] Zlib linking errors under 64bit Windows 7 (Holtgrewe, Manuel)

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

This data set came from the BFCounter program that introduced the Bloom
filter for filtering out erroneous k-mers
http://pritch.bsd.uchicago.edu/bfcounter.html

Here is a snippet of one of these file:
@EAS18:1:1:1:1:1119:0/1
NGTTACTTCGCGCTTTCACCGGAAGACGAAGCGCGCGATGCAGCGCGTCATATTCGTGACCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:1119:0/1 ltrim=1 rtrim=38
BTWa^`^``X^__bb_`_a]QX`\UW_H_\V^OZGZMZ_]RGWWGZTGZZWYT\GZX]_YWZBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:927:0/1
NGTAGCAAATCAAAAAGGTGGCGCTGGCAACGCTGGCGAGTGAGCCTAAATTCAGTGCCGCCGTCATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:927:0/1 ltrim=1 rtrim=32
B`\`bbbbabbb_[`bbYb`Zbbba[\b\bbab`X^\^[\GTbVH^\]XY[_VQQ_T^^a^]\]bba\BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:639:0/1
NACTTTTGCGGGAAGAATGGAAATAATATTAACGGTTTTAGTTTCTTGTTTGGTATTCAGTTGATCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:639:0/1 ltrim=1 rtrim=32
BbbbbbbZbbbbbbVbbbb`bbbbba^ab_^ab_]G]baa_\`aa[VTH^_KV`bb``^[U[H]H[RKBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:1479:0/1
NCCTTTCTGCGCTGCATTAACTTCCTCGAAAAACCGAGTGAAGGGTCGATCGTGGTCAATGGCCAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:1479:0/1 ltrim=1 rtrim=34
Ba^`aaaaa`abaaabbZ`[a]bbb[b]bbVa_bbbbb]ZY`aWMG^ab]baZZ\I_b`\MM[\aQBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:1131:0/1
NCGCATACATCAGCGAGAAACCGCCATCACGACGCGGATCGGTTGGCTCATACAGCTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:1131:0/1 ltrim=1 rtrim=42
BbUa_Y_b__`[_bZWQ_[Xab`bba`a_a]bb``_\\V[ZTIXGT_a_Z]^`MM\\[BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:1469:0/1
NGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAAATTGGTTTTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:1469:0/1 ltrim=1 rtrim=30
BaZbbbabaa`[`aa`_`[`babbb_ZQ_U]]_bb^a_W`aba]^\ZTb\W^^_SHT`I]H\QZJTbabaBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
@EAS18:1:1:1:1:989:0/1
NGAGTGAAACACCATTGCCAGAAAATCATTTACTGGATGCGCGGTTACGTAAAGAAAAAGAAGATGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+EAS18:1:1:1:1:989:0/1 ltrim=1 rtrim=31
Bbab]_bbbbbbb\baaab[]W\\a`bba`^Za`Y`[\abY`\_bZbbbW^aZVV`bbXSJa[`S[aa`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB



On 1/30/2013 6:00 AM, seqan-dev-request@lists.fu-berlin.de wrote:
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>    1. Re: Zlib linking errors under 64bit Windows 7 (Holtgrewe, Manuel)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 30 Jan 2013 10:14:31 +0100
> From: "Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>
> To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
> Subject: Re: [Seqan-dev] Zlib linking errors under 64bit Windows 7
> Message-ID:
> 	<FCCAB9D80C3DAB47B5601C5B0E62872B29435096@ex02b.campus.fu-berlin.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Theo,
>
> The FASTQ format is a good example for the file format fuzziness in bioinformatics. There is no real standard, only an article [1] telling what is there. The supplemental material is a tar.gz file that contains an example which says different ids for sequence and quality meta are an error.
>
> That said, what is the source of the FASTQ file? Ignoring the quality meta would not be a big change in the parser and be a change that I would be quite willing to make given that a "major" source of FASTQ generates such files.
>
> In a future version, such things should be configurable when reading FASTQ but alas we do not currently have time to make the change to make the I/O of sequences more configurable.
>
> HTH,
> Manuel
>
> [1] http://nar.oxfordjournals.org/content/38/6/1767
>
> ________________________________
> From: Theodore Omtzigt [theo@stillwater-sc.com]
> Sent: Wednesday, January 30, 2013 1:31 AM
> To: SeqAn Dev List
> Subject: Re: [Seqan-dev] Zlib linking errors under 64bit Windows 7
>
> 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 "EAS18:1:1:1:1:1119:0/1??????????????????????????" data_end=0x001757f6 "??????????????????????????" 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=38?????????????????????????????????" data_end=0x0017dc67 "?????????????????????????????????" 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?
>
>
>
>
>
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