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NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis
https://clara-parabricks.github.io/GenomeWorks/
Apache License 2.0
286 stars 76 forks source link

[cudamapper]: Print in SAM format #556

Closed nvvishanthi closed 4 years ago

nvvishanthi commented 4 years ago

Add outputting overlapped sequences + alignments in SAM/BAM format

closes !335

nvvishanthi commented 4 years ago

CC @tijyojwad

nvvishanthi commented 4 years ago

Two things to note here, which I'm kind of stuck on: 1) I was having some linker errors earlier on which I haven't got around to resolving :(. I think it's a cmake issue, but I'm not sure how to get it to work right. Probably also want to dynamically link it instead of statically link like I'm doing now 2) I found that the latest samtools master branch doesn't actually compile when I tried build using libhts-dev, so we might want to consider submoduling after all. Or maybe using a newer version

ahehn-nv commented 4 years ago

~I thought we decided to use a system installation of htslib instead of a submodule. What changed?~

ahehn-nv commented 4 years ago

Just saw your latest comment. I'm a bit confused - I thought we needed samtools' libhts, not samtools itself. Why do we need to compile the samtools?

nvvishanthi commented 4 years ago

@ahehn-nv I was having some linker issues which I think was due to my incorrect cmake so I tried to work around it (this is totally fixable, I just haven't figured it out what's wrong yet)). ~And then see 2) in my above comment about samtools not building properly with libhts-dev; not sure if we actually care about that or not, but I was able to get things working if I used htslib built from source~

nvvishanthi commented 4 years ago

I thought we needed samtools' libhts, not samtools itself. Why do we need to compile the samtools?

You're totally right, we don't need samtools itself. It was just a side-note, I suppose? I figured that since we wanted to be compatible with samtools, it would be bad if a library we were using was incompatible. Maybe it's not actually a problem. I can change to use libhts-dev after I figure out the linking issues I'm having

nvvishanthi commented 4 years ago

rerun-tests

nvvishanthi commented 4 years ago

@tijyojwad CI seems to fail because it's missing autoheader and autoconf. sudo apt install autoconf needs to be run first. Could these be added to the CI machines? I can add them to the System Requirements docs if acceptable

nvvishanthi commented 4 years ago

rerun tests