[Seqan-dev] Reading fastq records - missing records?
- From: Alexander Vowinkel <vowinkel.alexander@gmail.com>
- To: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Date: Mon, 1 Jun 2015 11:14:18 -0500
- Reply-to: SeqAn Development <seqan-dev@lists.fu-berlin.de>
- Subject: [Seqan-dev] Reading fastq records - missing records?
Hi Team,
here is another question:
Following code reads a fastq-file.
The file I'm testing on has 263333413 records:
$ zcat C563WACXX_1.fastq.gz | wc -l
1053333652
The problem is, that the code seems to only read
the first 4000000 records. I don't understand why.
Can you advise me here?
Thank you,
Alexander
PS: I removed try/catch for better readability
seqan::StringSet<seqan::CharString> ids;
seqan::StringSet<seqan::Dna5QString> seqs;
seqan::StringSet<seqan::CharString> quals;
unsigned batchSize = 10000;
do {
seqan::clear(ids); seqan::clear(seqs); seqan::clear(quals);
readRecords(ids, seqs, quals, inputFile, batchSize);
processRecords(ids, seqs, quals, barcodeGraph, vertexFilePtrMap);
totalProcessed += seqan::length(ids);
std::cout << "\r";
std::cout << "reads processed in total: " << totalProcessed;
std::cout.flush();
} while(seqan::length(ids) > 0);
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