v0.0.9

Fix bug in call to iterratereads_singleend with 1 proc

v0.0.8

Update setup.py entry points

Fully support single end reads

This version adds full support for single-end reads. Additionally, alignAndQuant is now directly accessible from the command line.

add bacon to setup.py

bacon_glm.py is now accessible from command line as 'bacon'

Fix assignreads import bug

This release fixes a bug where some necessary modules (mainly from assignreads) were not being imported.

Now conda installable (I think)

Packaging complete for conda installation

add setup.py for packaging

add setup.py for conda packaging

add GFF source argument

PIGPEN requires relating transcripts and genes. This is done using a supplied GFF file. The locations of the information in this file that are important for relating transcripts and genes (i.e. tags in annotations that denote transcript, parent and gene IDs) are slightly different depending on where this GFF came from. For mouse and human samples, we recommend using GENCODE gffs, but these are not available for other species. This release includes a --gfftype argument to handle this. The string supplied to this argument changes the getpostmasterassignments, assigntotxs, collapsetogene, readspergene, and writeOutput functions used. None of this comes into play if instead a bed file of genomic regions of interest is supplied via --ROIbed.

First release of PIGPEN

First release of PIGPEN