I know that Seqan 1.x is basically unmaintained, but we did get a significant looking set of test failures with gcc 10: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=980685 We only have one application in Debian that uses Seqan 1.x (dindel) and it is dead/archived by its authors.
The likely outcome is that both dindel and seqan 1.4.x will not be in the next release of Debian unless someone wants to fix the test failures.
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Helloooo. I'm struggling a bit with getting a random position in a random chromosome from an indexed BAM file, could somebody help me out? Here's what I've currently got:
using my_fields = seqan3::fields<seqan3::field::ref_id,
seqan3::field::ref_offset,
seqan3::field::cigar>;
seqan3::alignment_file_input alignment_file{alignment_file_path, my_fields{}};
uint8_t num_chr = alignment_file.header().ref_ids().size();
uint8_t rand_chr = rand() % (num_chr + 1);
uint64_t rand_pos = ???I'm just not too sure how to use ref_id_info and ref_dict with what I have above... I guess std::get<0>(ref_id_info) with the appropriate seqan3::field::ref_id should give me the length of the chromosome, but I don't know how to get this.
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Hello, so I want to pass a sam_file_input to a function and have a few questions regarding this:
I will be passing the variable via reference. This means that if I read two records from the file somewhere else, and then pass the file to another function, those two records will have already been read?
Secondly, I realized I can't simply do this: void foo(seqan3::sam_file_input & input_file), because the compiler wants the full template types. However, I don't want to give a specific list of fields, in case the function is used with different inputs which have different fields. Can I do the following?:
template<typename F, typename B>
void foo(seqan3::sam_file_input<seqan3::sam_file_input_default_traits<>, F, B> & input_file) {}I noticed that it does compile and my tests pass, but I want to know what the potential issues would be with this.
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For example, if I have the following code:
template<typename F, typename B>
void foo(seqan3::sam_file_input<seqan3::sam_file_input_default_traits<>, F, B> & input_file)
{
for (auto it = input_file.begin(); it != input_file.end(); ++it)
{
seqan3::debug_stream << (*it).id() << '\n';
}
}But the function is called with a
sam_file_input<seqan3::sam_file_input_default_traits<>, seqan3::fields<seqan3::field::cigar>, seqan3::type_list<seqan3::format_sam>>then will the compiler give an error that seqan3::field::id is not present? Or do I have to add the line if ((*it).has_value()) before the printing.
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Has anyone experience with SeqAn3/ranges and gcc 9.1? I tested with a later gcc9 version (also don't have another one installled yet) and had no issues but a reviewer encountered the following problem which seems to come from the ranges library when building
…/seqan3/submodules/range-v3/include/range/v3/range/concepts.hpp:56:5: internal compiler error: in nothrow_spec_p, at cp/except.c:1247Just wondering whether there ever have been issues with a certain compiler version
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I am trying to use rabema to evaluate my output. I ran razers3 on hg38 with 100'000 queries. This created a out_gold.sam (4.5GB). Using rabema_prepare_sam I converted it to out_gold.prep.sam (15GB). But converting it to a bam file samtools view -Sb out_gold.prep.sam > out_gold.bam fails. I don't really know where to start searching. The error message:
...
[W::sam_hdr_create] Duplicated sequence "" in file "out_gold.prep.sam"
[W::sam_hdr_create] Duplicated sequence "" in file "out_gold.prep.sam"
[W::sam_hdr_create] Duplicated sequence "" in file "out_gold.prep.sam"
[E::sam_hrecs_update_hashes] Duplicate entry "" in sam header
samtools view: failed to add PG line to the headerThe resulting out_gold.bam file is only 28Bytes large.
I am following the instructions from here: https://github.com/seqan/seqan/tree/develop/apps/rabema
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