spaln
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ogotoh
Genome mapping and spliced alignment of cDNA or amino acid sequences
Fixes https://github.com/ogotoh/spaln/issues/67 This is a PR that uses https://github.com/DLTcollab/sse2neon/ to translate SSE to NEON. It basically disables the usage of arm_neon.h and uses the sse4.1 impls for aarch64. If the...
Hello, I am trying to build Spaln on Linux ARM64/aarch64 and it [fails](https://github.com/bioconda/bioconda-recipes/pull/47400) with: ``` $BUILD_PREFIX/bin/aarch64-conda-linux-gnu-c++ -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O3 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/spaln-3.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -Wl,-O2 -Wl,--sort-common -Wl,--as-needed...
It tests the build on - Linux x86_64 - passes ! - Linux aarch64 (ARM64) via emulation (QEMU) - currently fails !
$./configure Checking for 64 bits compiler... use CXX=g++ CFLAGS=-O3 -march=native binaries install to /home/ubuntu/bin tables install to /home/ubuntu/table alndbs install to /home/ubuntu/seqdb wrote Makefile wrote files OK. try make and...
first of all i would like to thank you for adding support for adding support for staged install as suggested in issue #61. binaries produced by current Makefile lack common...
I'm trying to build spaln v2.4.12 with GCC 10.2 and using "`-O2 -march=native`" as compiler options. This fails with: ``` g++ -O2 -ftree-vectorize -march=native -fno-math-errno -Wall -DM_THREAD=1 -DUSE_ZLIB=1 -c fwd2b1.cc...
Hi, We recently used spaln (version 3.4.13f) to align CDS sequences (~25,000 sequences) to a genome(~450Mb) on Centos 8 system (Our server has 1T of memory) . But we encountered...
Dear @ogotoh, I have mapped protein sequences to a genome and observe in the alignment output (O1) that many codons that I expect to encode "S" or Serine are written...
i am trying to build and package spaln for [BioArchlinux project](https://github.com/BioArchLinux/Packages). i have ran into issues at the actual package creation step. Arch Linux build script relies on [gnu make's...
Hi, With the following command I get 'segmentation fault (core dumped)' when multi-threading: spaln -Q4 -O1,2 -t10 -M5 -T -dPH_PH_racon_pilon_pseudohap_masked uniprot_arth_blattodea.faa > spalnout No such error occurs with -t1. I...
