abhinav

fixes bowtie2-build TypeError in PyPy

3

This is a band-aid for an error encountered when at least one version of PyPy is the default version of Python: ``` bowtie2-build --version Traceback (most recent call last): File...

uses FileSystem's listStatus rather than FileInputFormat's in LzoInputFormat

3

Proposed resolution to #426, which describes how FileInputFormat's listStatus is slow on S3 for input paths spanning many files.

LzoInputFormat's listStatus() can take prohibitively long on S3 because it invokes FileInputFormat's listStatus() implementation

11

LzoInputFormat's listStatus begins with ``` java List files = super.listStatus(job); ``` where super refers to FileInputFormat. FileInputFormat's listStatus() calls singleThreadedListStatus() (when LIST_STATUS_NUM_THREADS == 1), which is not optimized for S3....

In local mode, L1750 of `emr_simulator.py` creates a temporary directory in `/tmp` when it should do this in the scratch directory specified by the user

Add specification of expected precision and recall on dataset as command-line parameters of `line.py` and return failure of they don't agree with test output; this way, changes to the underlying...

add counters for debugging

1

"ideas for counters we'd like to have (a) how many reads/readlets align, (b) number of introns called, (c) number of introns & nucleotides that go into intron index"

- Resolve multimapping reads in a way that makes the most sense for downstream analyses. (How? Push coverage distribution toward more uniformity like MMR?) - Add option to run job...