seryrzu / unialigner Goto Github PK

It seems that running the tool without any arguments just outputs the following:

$ ./tandem_aligner
Incorrect parameters
first missing

And running with -h or --help yields the same message:

$ ./tandem_aligner -h
Incorrect parameters
first missing
$ ./tandem_aligner --help
Incorrect parameters
first missing

It might be good to update things so that it prints a descriptive usage message (even just the one that's here in the README) when the user runs it without args and/or with -h/--help

Hi,

would you please add unialigner to bioconda clound, it's difficult to install on some old machines.

Best,
Kun

Hi,

Is possible to output SAM or PAF for two sequence alignments? The default only has CIGARs which cannot use for dot plot. How do you plot synteny with CIGAR in paper?

Hi!

Is it possible to provide a VCF with e.g. indel variants -> Extract reads of these specific region that contains the indel -> feed them to TandemAligner and get back a corrected VCF?

Hi,

Is it possible to convert unialigner results to some other readable format like bed paf or sam? I want to know the overlap region of two sequences, not just cigar or dotplot.

Best,
Kun

Hey, Andrey! Hope you've been well; it's been a while 😄

Just a heads up that the README says the following to compile:

git clone [email protected]:seryrzu/unialigner.git
cd unialigner/unialigner
make -j4

But I think the unialigner subfolder in the repo is currently named tandem_aligner (probably missed during the renaming?). I would open a PR, but renaming the folder where all the source code exists would probably create conflicts with any further development you've done, so I'll just make an Issue and let you resolve it 😄

Thank you for developing Unialigner, an alignment tool suitable for highly repetitive sequences. I have successfully installed and run it, but based on my test results, it uses a right-aligned strategy. Since this will lead to incomparability with other alignment tools, is it possible to add parameters to provide the possibility of left alignment?

what's the matter?
cmake：3.15.7 or 3.19.8
gcc：8.3.1

thanks

Hello,

I am trying to install on CentOS7 and ran into some issues.
I cloned the github repo, loaded gcc/8.2.0 and cmake 3.17.3, cd into tandem_aligner/tandem_aligner and ran make -j4
and I am receiving these errors

in tandem_aligner/tandem_aligner/src/tools/suffix_array/suffix_array.hpp:27:41:

error: ‘max_element’ is not a member of ‘std’
         value_type alphabet = 1 + *std::max_element(str.begin(), str.end());

in tandem_aligner/tandem_aligner/src/projects/rare_kmer_aligner/rare_kmer_aligner.hpp:76:32:

error: ‘const class std::unordered_set<__int128 unsigned, std::hash<__int128 unsigned>, std::equal_to<__int128 unsigned>, std::allocator<__int128 unsigned> >’ has no member named ‘contains’
                 if (rare_kmers.contains(hash)) {

Let me know if I can provide any additional information and thanks in advance!

I get this error when I try to use this tool. Any clue what is happening?

=== Stack Trace ===
/unialigner/tandem_aligner/build/bin/tandem_aligner(+0xdff9) [0x55f21bd66ff9]
/unialigner/tandem_aligner/build/bin/tandem_aligner(+0x1eb0b) [0x55f21bd77b0b]
/unialigner/tandem_aligner/build/bin/tandem_aligner(+0xa5a9) [0x55f21bd635a9]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7ff30e559d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7ff30e559e40]
/unialigner/tandem_aligner/build/bin/tandem_aligner(+0xaad5) [0x55f21bd63ad5]
tandem_aligner: /unialigner/tandem_aligner/src/projects/tandem_aligner/tandem_aligner.hpp:186: void tandem_aligner::TandemAligner::Find(const std::experimental::filesystem::v1::__cxx11::path&, const std::experimental::filesystem::v1::__cxx11::path&) const: Assertion `first_vec.size()==1' failed.
/var/lib/slurm/slurmd/job1336413/slurm_script: line 16: 879706 Aborted                 (core dumped) /unialigner/tandem_aligner/build/bin/tandem_aligner --first "/output/2_GFATOOLS_RESULTS/1_3_23_R1041_DORADO_v0.4.1_400bps_SUP_v4.1.0_SIMPLEX_DUPLEX_UL_HG002_3_MIN5000/1_3_23_R1041_DORADO_v0.4.1_400bps_SUP_v4.1.0_SIMPLEX_DUPLEX_UL_HG002_3_MIN5000.asm.bp.hap1.fasta.gz" --second "GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta" -o "/kkyriaki/unialigner"