parameter check for WFA?

[vpbrendel]

Nice code. Thank you. But:

Could you provide a simple set of tests with defined inputs and outputs? I could not get a single run (with arbitrary toy genome FASTA files) to work to the end.

wfmash --version v0.13.0-0-gd7b6960

All runs end with [WFA::Penalties] Penalties (X=0,O1=5,E1=8,O2=2,E2=49) must be (X>0,O1>=0,E1>0,O1>=0,E1>0)

Seems like a simple error in the code, yes? Even the "must be" part looks off (should mention O2 and E2). I realize that the latter is in the WFA2-lib repository, but I think this is still in your team effort.

Thanks, Volker

[AndreaGuarracino]

@vpbrendel how did you install wfmash?

[vpbrendel]

On Fedora 40:

# wfmash
#
cd /usr/local/src
git clone --recursive https://github.com/waveygang/wfmash
cd wfmash
git submodule update --init --recursive
cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-Ofast' -Bbuild && cmake --build build --
ln -s /usr/local/src/wfmash/build/bin/wfmash /usr/local/bin/wfmash

[vpbrendel]

Problem solved. My post was incomplete as it were. I had followed installation of wfmash with installation of vcflib. The latter links to an older version of WFA2-lib (ab690aa). My installation code made that library version default, and wfmash then gave the reported errors. Collateral damage of not properly understanding your entire ecosystem of useful programs (thanks again for all this!). Below are working installation instructions. Volker

# htslib
#
cd /usr/local/src
git clone https://github.com/samtools/htslib htslib
cd htslib
git submodule update --init --recursive
make && make install
echo "/usr/local/lib" >> /etc/ld.so.conf.d/libc.conf
ldconfig

# wfmash
#
cd /usr/local/src
git clone --recursive https://github.com/waveygang/wfmash
cd wfmash
git submodule update --init --recursive
cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-Ofast' -Bbuild && cmake --build build --
ln -s /usr/local/src/wfmash/build/bin/wfmash /usr/local/bin/wfmash

# vcflib
#
cd /usr/local/src
git clone --recursive https://github.com/vcflib/vcflib.git
cd vcflib
mkdir -p build && cd build
cmake -DCMAKE_BUILD_TYPE=Debug -DZIG=OFF -DOPENMP=OFF ..
cmake --build .

export PATH=$PATH:/usr/local/bin
export PATH=$PATH:/usr/local/src/vcflib/build

[ekg]

Thanks for the follow up! If alignment isn't working on a test example sometimes the problem is that the example is very short. But here it looks like a different issue.

On Mon, Apr 1, 2024, 14:45 Volker Brendel @.***> wrote:

Problem solved. My post was incomplete as it were. I had followed installation of wfmash with installation of vcflib. The latter links to an older version of WFA2-lib (ab690aa). My installation code made that library version default, and wfmash then gave the reported errors. Collateral damage of not properly understanding your entire ecosystem of useful programs (thanks again for all this!). Below are working installation instructions. Volker

htslib

# cd /usr/local/src git clone https://github.com/samtools/htslib htslib cd htslib git submodule update --init --recursive make && make install echo "/usr/local/lib" >> /etc/ld.so.conf.d/libc.conf ldconfig

wfmash

# cd /usr/local/src git clone --recursive https://github.com/waveygang/wfmash cd wfmash git submodule update --init --recursive cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-Ofast' -Bbuild && cmake --build build -- ln -s /usr/local/src/wfmash/build/bin/wfmash /usr/local/bin/wfmash

vcflib

# cd /usr/local/src git clone --recursive https://github.com/vcflib/vcflib.git cd vcflib mkdir -p build && cd build cmake -DCMAKE_BUILD_TYPE=Debug -DZIG=OFF -DOPENMP=OFF .. cmake --build .

export PATH=$PATH:/usr/local/bin export PATH=$PATH:/usr/local/src/vcflib/build

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