Brent Pedersen

I think it should be straight-forward to support CRAM in covstats, I'll just do a system call to samtools view. I'll have a look at this next week if not...

I just had a look at this and the cram index does not store the total number of mapped reads so it's not possible to estimate the coverage like that...

given the lack of cram parser in go, I don't plan to support this. It's possible to get actual coverage for a 30X WGS cram in < 5 minutes using...

Actually, I forgot what it was doing. It makes a system call to samtools which converts cram to bam, then parses the bam. So the sampling stuff (the parts that...

I suppose I could make it calculate the mean for the first part of the chromosome with covstats. As soon as you starting converting to bam, you're going to be...

where is the benchmark?

See: https://gist.github.com/brentp/fecdc6d1c16cde4992d96d7c7a205166

Thanks for the analysis. I was more concerned with the Query time than the creation. Re this: > That does not seem right. Let us rewrite this code... > >...

wow. thanks for taking a look. here is what I see: ``` lookup-8 ... time = 0.067491 s lookup-64 ... time = 0.056205 s (speedup: 1.20) bit-parallel ... time =...

thanks for the explanations. I checked samtools/bcftools and htslib and there is no code that uses nonzero value `is_copy`. when I use that in my code with the expected lengths,...