Rob Patro

Hi all (@Gaura / @gmarcais), While this has languished somewhat as we try to figure out what regex engine to include and how best to package it, I wanted to...

Hi @Gaura and @gmarcais, Just an update, this approach currently seems to be working. We can stream sciseq3 data through our `seq_geom_xform` tool to convert it to a standard "normalized"...

It is possible to output gene counts directly, but using `tximport` is the preferred and officially supported method. The reason for this is that the gene-level aggregation built into salmon...

This *usually* means that the version of the boost library you have was not compiled with a C++11-compatible ABI. There is a incompatibility between pre C++11 and post C++11 `std::string`...

Hi @adamrtalbot, Thanks for pinging me here. I'm tagging @mikelove here too in case he has specific thoughts / input. Basically, when we first added the feature to deduplicate reference...

Hi @ggraham, Thanks for this effort! One other thing covered in the patch that I haven't checked in the fork yet is the ability to compile under clang. This is...

Hi Garrett, Yup; the intent is to compile cleanly with GCC on Linux x86 and with Clang OSX x86 and ARM. I suppose there's no reason not to work with...

pinging @mikelove, who might have some insight on the `tximport` behavior here (or if the issue likely resides elsewhere).