Benjamin Langmead

Yes, I noticed this recently as well. Up to now we've tried not to force a choice of C++11 versus pre-C++11, but this recent change broke that. @ch4rr0 and I...

+1 to this idea. This code in James Taylor's repo might help: https://bitbucket.org/james_taylor/bx-python/src/8600c7055ed08e87c6951e65ccce6771b38d0acf/lib/bx/bbi Ben

This is low priority

Maybe you have this already? I see `"Tags": [],` in the output JSON, but there are function in the code that have `tags=''` in the parameter list, so I assumed...

I wish there were a global mechanism whereby individual tasks can report "catastrophic error 4675 happened and here's some text describing it," then some global process aggregates those, collapses identical...

+1

It turned out that the variability I was seeing was probably because of the empirical read/fragment length distribution and a problem with how it's used in the bias correction code:...

This is subsumed by other changes made since

I can unravel at least 1 level of the mystery, which is that we use this file to determine what to download: https://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt And the mentioned genome seems not to...

Thank you -- we are looking into this. I suspect the mention of `` is a spurious hold-over from the Bowtie 1 manual, and that we should have said ``...