Every so often (way more often than seems reasonable) reads are delivered to me unsorted by read name. This happens pretty often with reads downloaded from NCBI as well. I added a config option to sort reads by name using bbmaps read sorter, which seems to be efficient in my experience.
It's fast enough that I almost wonder if it should be the default to sort reads, but I guess for most use cases, it's best to have it be user-defined.
It's a little inelegant how I set it up, just a bash ifelse statement, but it works...
Every so often (way more often than seems reasonable) reads are delivered to me unsorted by read name. This happens pretty often with reads downloaded from NCBI as well. I added a config option to sort reads by name using bbmaps read sorter, which seems to be efficient in my experience.
It's fast enough that I almost wonder if it should be the default to sort reads, but I guess for most use cases, it's best to have it be user-defined.
It's a little inelegant how I set it up, just a bash ifelse statement, but it works...