broadinstitute/viral-ngs — pull request #32 by iljungr (2014-11-06 16:47:17+00:00)
Title: Irwin taxon filter interfaces

- Changed interfaces to partition_bmtagger and dup_remove_mvicuna to require explicit specification of both fastq files for paired-end reads.
- Defined interfaces for deplete_blastn so that you can plan their use in the overall pipeline. I expect to implement them today or tomorrow. Here's a summary of the 4 utilities in the deplete_blastn suite; details can be found in the code.
The first one, deplete_blastn uses blastn to remove reads that match
a set of databases, all in one step.
The other three break the same operation into several steps allowing the
caller to run them in parallel if appropriate infrastructure is available.
The different pieces communicate by way of a single directory,
scratchDir, which they create, fill, and delete.
deplete_blastn_prep: splits file into several pieces and prepare for blastn
deplete_blastn_do1: runs blastn on one of the pieces with one database
deplete_blastn_finish: combines the results and does postprocessing