Heng Li

@hnnd Could you try chromap-0.1.3-asan_x64-linux.tar.bz2 from the [download page](https://github.com/haowenz/chromap/releases/tag/v0.1.3)? The precompiled executable is a debug build that may report extra information on segfault. That executable runs slower and uses more...

What does SALSA2 require? What does its input BED look like?

An effective heuristic is to intentionally penalize mapq if the alignment length is short and/or the alignment contains few seed hits. The reasoning behind is that it is more likely...

There *might* be a few potential issues with the bioconda recipes: 1. bcftools and tabix are not updated. 2. samtools doesn't depend on htslib. 3. "make test" is not used,...

Conda is a package manager for precompiled binary packages, but is linux-distribution agnostic and does not require the root privilege. Bioconda is built on top of conda and provides bioinfo-related...

> since UNIX pipe cannot do either unget or seek, thus once the program detect the data should be handled by htslib, it's too late to handle off the FD....

> the bedtools actually detects file format like a gziped bam or even a bam that has been compressed multiple times Ok, I agree wrapping hFILE won't achieve these functionalities...

I usually don't like the majority rule on specification. Depending on the type of the issue, the majority don't necessarily make the best choice. It would be good for everyone...

I want to echo @ktan8's point b). With Q20 chemistry, the accuracy of Nanopore is approaching the human heterozygosity. The differences between the reference and the training individual will start...

That is great, and should address @ktan8's point a) as well. It would be good to also have enough low-complexity sequences in the training set. These low-complexity sequences can be...