hubward 0.2.2

Overview

This poster gives an overview of hubward, and provides a worked example.

Further details can be found in the full documentation.

0.2.2 (2016-01-20)

• Support for liftover of BAMs (includes a workaround for Crossmap bug that segfaulted on liftovers with a specified output filename in the test environment).

• When lifting over between assemblies and the source assembly doesn’t match what is configured for a track, raise a ValueError.

• For lifted-over studies, the metadata.yaml config keeps track of the liftover history in the new study/liftover section

• improved test environment setup

• improved tests (checking for existence of uploaded files)

0.2.1 (2015-12-05)

• if the description field is empty or missing, fill in the contents of README as documentation.

• add functools32 to requirements.txt (thanks Titus Brown)

• fixes to hubward liftover:

  • downloaded chainfiles are cached

  • skip tracks where assembly of track differs from the requested –from_assembly

  • upon lifting over, add a note to the description of the study’s metadata.yaml to reflect this and also as a comment in the YAML file.

  • workaround for a bug in CrossMap on BED9+ files. The thickStart and thickEnd fields were not being lifted over correctly.

• use pycurl for downloading for better handling of URL redirects. This happens, for example, when downloading supplemental data from ScienceDirect

• less verbose bigbed/bigwig conversion

• allow optional fields in metadata to be blank

• improvements to testing framework

0.2.0 (2015-10-24)

Streamlining of the code and CLI. This causes some backward incompatibility with metadata.yaml config files in version 0.1.0, in particular, the “source” section is now required. There is now a defined schema for the metadata and the grouping files so that future changes can be validated and automatically fixed.

0.1.0 (2014-01-11)

• First release on PyPI.