Daniel Standage

I'm -1 on any big changes for the time being. Yes, the OS X Travis builds are the big pain point right now. It's not that the build itself takes...

Hi @UltraSpecialException! It looks like you're installing khmer in a python 2 environment. We recently stopped supporting Python 2, so khmer requires Python 3.4 or higher. Sorry the default installation...

Hi Solshi! Could you please describe with a bit more detail what the contents of the NSV will be and what sequence characteristics they will summarize? An example of what...

Closed by `abundance-dist-single.py` ages ago, amirite?

The current docstring actually documents the function pretty well. ``` """Read pairs from a stream. A generator that yields singletons and pairs from a stream of FASTA/FASTQ records (yielded by...

Yeah, I think it would be clean and easy to add a clearly marked "backwards compatibility" section to the `khmer/__init__.py` file with a few such definitions. Let me know if...

Hi @brooksph! How was this reads file created? Was it downloaded or converted using the SRA toolkit? I'm pretty sure this is the standard defline format for `fastq-dump`, which, if...

Oops, my fault. The IDs from @brooksph's example have 3 period-separated values: - `X`: accession - `Y`: serial number - `Z`: pairing info ``` SRR606249.9162938.2 | | | |---X---| |--Y--|...

> Is there a way to use pybbhash on existing kmer graphs created by khmer? I don't think so. The hashing strategy is quite different between khmer and the MPHF...

Some relevant lines from the Makefile. ``` $(EXTENSION_MODULE): $(CPPSOURCES) $(CYSOURCES) ./setup.py build_ext --inplace ``` So the Cython extensions are compiled and bundled into the khmer shared library by `setup.py`. Any...