qapa v1.3.0

This release contains new functionality and improvements to the build and fasta sub-modules. The main highlight is support for PolyASite version 2 that should benefit users of human and mouse libraries. The quant sub-module is unchanged from previous versions.

Pre-compiled libraries for hg38 and mm10 are available for download below.

• hg38 sources: GENCODE V31 Basic, GENCODE Poly(A), PolyASite V2, and Ensembl Genes V97
• mm10 sources: GENCODE VM22 Basic, GENCODE Poly(A), PolyASite V2, and Ensembl Genes V97.

Changes:

• Python 2 is no longer supported in this release (https://www.python.org/doc/sunset-python-2/). The last working version with Python 2 is v1.2.3.
• Add support for PolyASite version 2 (gets auto-detected). (#22)
• Replace log messaging with logging framework
• Add --debug option for increasing verbosity of log messages
• Add parallel processing to some stages of build that should help improve runtime. Can be controlled using --cores option (defaults to using all available cores).
• Deprecate -H option for custom genePred files as they are now auto-detected.
• Deprecate --dist5 option for merging 5’ ends. This option was never actually used.
• More unit tests
• Fix bug in fasta sub-module where duplicate sequences were not being properly detected based on identifier.