Re: [Seqan-dev] Reading fastq records - missing records?

[Alexander Vowinkel <vowinkel.alexander@gmail.com>]

Hi Fadhlan,

why should memory be an issue?

I can load 400 of 10000 sized batches.

I always clear the Sets that save the sequences

after they were used.

Best,

Alexander

2015-06-02 23:36 GMT-05:00 Fadhlan Rizal <fadhlan.fari@gmail.com>:

i dont know why, but maybe because your memory doesn't enough?

2015-06-01 23:14 GMT+07:00 Alexander Vowinkel <vowinkel.alexander@gmail.com>:

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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