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Questions tagged [seqan]

SeqAn is a C++ template library for the analysis of biological sequences.

SeqAn is the C++ template library for the analysis of biological sequences. It contains algorithms and data structures for

  • string representation and their manipulation,
  • online and indexed string search,
  • efficient I/O of bioinformatics file formats,
  • sequence alignment, and
  • much more.
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C++ Template Metaprogramming - Is it possible to output the generated code?

I would like to debug some templated code to understand it better. Unfortunately I'm new to template metaprogramming and it IS hard for me to get in. When I try to output the preprocessed source files I get 125 000 lines of code :/ So is there a way…
n00ki3
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Multiple sequence alignment with gaps in input (Seqan)

I have a sequence of strings like so: ["123-5", "1-45", "--345"]. In result is perfect to get 12345. So sometimes I know that in certain position I have symbol, but do not know which. From examples I get this code. typedef String TSequence; …
Gralex
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Online Pattern search over StringSet

The SeqAn tutorial for Pattern Matching mentions that StringSet's can serve as either haystacks or needles. In attempting to use a StringSet as the haystack as follows, StringSet seqs; /* do stuff to load sequences into seqs…
merv
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what is this C++ deserialization idiom? calling a file-reader function with an integer ID variable as `reinterpret_cast(&id)?`

I'm reading through the internals SeqAn library (which handles biology-specific file formats and data structures) and I'm coming across what must be a c++ idiom which I don't quite understand. There's a unique id variable record.rID that is an…
daj
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SeqAn C++ library : different rID values for bam vs. sam with identical data, bam results in assertion failure due to length of namestore

I'm using seqan 1.4.1 to read sam/bam files. I have a sam and bam file from the same data (an alignment to rn5 refseq genes). Oddly enough I didn't get this error when I aligned to ensembl genes. I am reading the sam/bam files BamStream, but the…
daj
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What is this piece of c++ code doing?

I don't know how and why this piece of code works: // postorder dfs Iterator< Index >, TopDown > >::Type myIterator(myIndex); while (goDown(myIterator)); for (; !atEnd(myIterator); goNext(myIterator)) // do…
n00ki3
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Seqan mini-bowtie example not compiling

I try to copy the example of mini-bowtie from the Seqan Web site. Note that the example comes from version 1.4.2, not the current one. When I compile, I have an error. The minimal reproducible example is: #include #include…
unamourdeswann
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How to create an index out of a file?

Is is straightforward to create a index out of a String object for example : typedef Index TIndex; TIndex index("How much wood would a woodchuck chuck?"); In my case, I have a large file. One obvious way is to load the text in the…
user2370139
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An example of template subclassing

I was reading SEQAN documentation. In Getting Started section, they mentioned "Template Subclassing" as a method to overcome runtime polymorphism overhead. OOP vs. Generic Programming: In SeqAn, we use a technique called template subclassing…
Zingo
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Private member variable is null when passed from constructor to member function

I'm pretty new to OOP in c++ so bear with me here. In my header that defines my member variables; class AntibodyJunction { private: //raw seq seqan::Dna5 _raw_sequence; //private funcs void…
jwillis0720
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