alienzj

@anpin Thanks. Yes, my current repository is set to https://github.com/alienzj/.jupyenvrc. I will follow your suggestions soon.

Sorry for my misunderstanding. From the CMakeLists.txt file https://github.com/ablab/spades/blob/main/ext/src/bwa/CMakeLists.txt#L33, it appears that SPAdes does not use the most recent version of BWA, but instead includes a method to build BWA...

``` [ 96%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/main.cpp.o [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/series_analysis.cpp.o [ 97%] Building CXX object projects/spades/CMakeFiles/spades-core.dir/__/mts/contig_abundance.cpp.o [ 97%] Linking CXX executable ../../bin/spades-core /usr/bin/ld: ../../common/alignment/libalignment.a(bwa_index.cpp.o): in function `alignment::BWAIndex::AlignSequence(Sequence...

Unfortunately, SPAdes used: https://github.com/ablab/spades/blob/main/src/common/alignment/bwa_index.cpp#L377 https://github.com/ablab/spades/blob/main/ext/include/bwa/bwamem.h#L153 BWA used: https://github.com/lh3/bwa/blob/master/bwamem.h The API is not the same one. It is difficult to use lh3's BWA directly at this moment.

I checked the API more in depth, basically, `mem_align1` did same thing when compared to `mem_align1_bin`.

2020, why has this still not been implemented?

Still 2020, but I'm sure we will get it very soon :-)