GASAL2
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nahmedraja
Hi，as the introduction said ,GASAL2 seems to support the one-to-all alignment method,is there a example about that?I‘ve tried to find the method through the test example but it couldn't help.Looking...
I looked through your github but I couldn't find the nvbio github that you used for the benchmarking in the GASAL2 paper. Can you make that code available? Thank you...
Hello. I just installed GASAL2 on the CHPC system at University of Utah. I followed your instructions and then ran the test_prog.out on the given test data and had this...
I was just wondering if the code was available for the BWA-mem/Gasal2 integration?
Hello, I could successfully compile GASAL2 using the configure.sh and then make, but I am experiencing issues to compile test_prog. Below there is a part of the output when executing...
Hello, I have been running into an issue where GASAL2 fails with a CUDA memory error on some datasets (but not all) when I use traceback. In my analysis, it...
After compiling the code with ```bash ./configure.sh $CUDA_HOME make GPU_SM_ARCH=sm_60 MAX_QUERY_LEN=1024 N_CODE=0x4E cd test_prog make ``` I run: ``` ./test_prog -p -y local query_batch.fasta target_batch.fasta ``` This raises several CUDA...
The `-y` option to `test_prog` does not have the ability to enabled the banded alignment kernel. Is this intentional?
N_CODE can differ from N_VALUE because N_VALUE holds only the bottom nibble of N_CODE. [This line](https://github.com/nahmedraja/GASAL2/blob/master/src/kernels/pack_rc_seqs.h#L115) uses `N_CODE`, but it should use `N_VALUE`.
[These lines](https://github.com/nahmedraja/GASAL2/blob/master/src/kernels/pack_rc_seqs.h#L111-L116) count the number of `N` in the last word; however, if `N` can be used in sequences generally (which seems to be a design goal), then this is...