Ryan Lorig-Roach
Ryan Lorig-Roach
Not sure if this is intentional or not, but there are two fields in the BamAlignment class which seem to be oversized: https://github.com/pezmaster31/bamtools/blob/2bd8699bbb8e2f1fb0677d44049bddbb7fe39419/src/api/BamAlignment.h#L135 https://github.com/pezmaster31/bamtools/blob/2bd8699bbb8e2f1fb0677d44049bddbb7fe39419/src/api/BamAlignment.h#L136 mapq has a maximum value of...
Hi, for my purposes, I need to parse many alignments, but I don't much care about the cigar, or read sequence, or tags. However, I do need the read names....
Hi, Thanks for this nice contribution to the graph alignment community. I am working on integrating it to one of my pipelines and I get an error on the first...
Hi, I tried to create a dafsa object from the output of dafsa: ``` from dafsa import DAFSA def main(): lines = [ "+-- #5: n(#6/2:/2) [('p', 6)]", "+-- #6:...
I've been using paths quite a lot in bdsg and found that a couple methods would simplify things: ``` pop_path_front/back rename_path ``` Based on the existing methods `prepend_step` and `append_step`,...
Specifying `BUILD_STATIC=ON` doesn't actually create static libs when using CMake: ``` ExternalProject_Add(project_bdsg GIT_REPOSITORY https://github.com/vgteam/libbdsg.git PREFIX ${CMAKE_SOURCE_DIR}/external/bdsg/ CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_SOURCE_DIR}/external/bdsg/ -DBUILD_STATIC=ON -DRUN_DOXYGEN=OFF -DBUILD_PYTHON_BINDINGS=OFF BUILD_IN_SOURCE True INSTALL_COMMAND make install ) ``` results in:...
Hi, Since you have a working knowledge of minimap's code base, is there any chance of creating a more user-friendly interface that people could call from their own C++ or...
Hi, I'm attempting to link your library with a combination of `FetchContent` and `add_custom_target`. Everything installs great, but when I link KMC (the one built by your CMakeLists) in order...
Hi, thank you for the lovely software and informative publication. Do you still have plans to extend vcfdist to evaluate unphased VCFs, as you indicated in your paper? As part...
Hi, Do you have any plans to produce a GFA output instead of a Fasta? it would be a natural way to represent the full graph with adjacency information betw...