Rob Patro

Hi @daviesrob, Thanks for the quick reply. I build htslib with a regular `./configure --prefix= && make install`. I am building these together for our project [Salmon](https://github.com/COMBINE-lab/salmon). We use some...

Hi all, I realized the awesome [SeqLib](https://github.com/walaj/SeqLib#integrating-into-build-system) library links both libbwa and libhts. So, I dug into things a little bit, and realized they actually had to hack the kstring.c/kstring.h...

BWA-MEM2 relies heavily on x86 (specifically, Intel, I believe) intrinsic instructions. I can't imagine porting it to have M1 support would be easy (or even something the developers would want...

Hi @mej54, First, thanks for using salmon and for providing detailed feedback! There are two main points I'd like to make in response to the points you raise. First, v0.9.1...

Hi @avocado851, No worries, and welcome to the RNA-seq analysis world! Thanks for choosing salmon :). There's a detailed discussion over in [this](https://github.com/COMBINE-lab/salmon/issues/533) issue describing some reasons you might be...

Hi @seanken, Thank you for reporting this. I agree this error message should always show up. My guess is that this is related to the fact that the error is...

Hi @ACastanza, Thanks for reporting both of these. For the first, I think it is just the case that the message needs to be updated. In fact, the `--validateMappings` flag...

Thanks for the report @callumparr! I'll ping @gmarcais on this.

Hi @Kisekya, I wonder if you could say something about how the BAM file itself was prepared. The `MU` library type is quite exotic and certainly not expected for a...

Hi @Kisekya, So BWA-MEM and BWA-MEM2 are somewhat of a problem to begin with because they perform local alignment, which isn't really ideal for aligning RNA-seq reads to the transcriptome....