Simon Ye

open_or_gzopen -> compressed_open. Add support for zstd.

2

Zstd has a nonstandard python api which requires customization. Also allows for multithreading compression.

Changes spades default mode from rna to meta

1

The rnaSpades mode is heavily focused on mRNA transcriptome assembly and is very aggressive at splicing assemblies into short transcripts. The —meta mode would be more suitable for our DNA/RNA...

Kraken2 depletion for human reads as alternative to bmtagger

2

* Add `kraken_unclassified` command that combines p filtering with depletion * Less sensitive than bmtagger (tradeoffs) but much faster. Can be controlled with p. p=0.01-0.05 a close to bmtagger but...

Split out TaxonomyDB into a separate python lib

1

New python lib ncbitax

Split out taxonomy into separate python package

1

The taxonomy code is getting fairly large in `metagenomics.py` and should be split out into a separate python package.

Add OS X testing on travis

5

It looks like it is now generally available and default: travis-ci/travis-ci#2320

Previously would only cluster perfect matches except for mismatches close to the end (~10 bp) Addresses #31

Normally the output is in shuffled blocks due to random OpenMP ordering. Use the ordered pragma of OpenMP for ordered output (incurs a performance penalty for synch).

Add functionality to load a database catted into a single file instead of from multiple files from a directory. This combination allows the workflow of loading the database from a...

Also add diagnostic msg to mmap'd quickfiles to print % cached already.