1.9

Many updates to do with UMI counting, handling reads from newer sequencing machines, and statistical refinements. See the file "CHANGES".

1.8

Remove dependency on pysam, and related error if pysam present.

1.7

v1.7

Namespace bugfix

1.6

v1.6

R code cleanup

1.5

STAR aligner is now used.

1.3

Major changes are allowing extension over non-pure genomic As and filtering of peak with short average tail length.

1.1

Change to poly(A) calling in reads: no longer attempt to use quality information. poly(A) tail is called as a sequence of 10 or more bases of A and/or adaptor sequence.

No longer outputs "deduplicated" results.

0.42

0.42 release. Remove some excess memory usage. Tweak gene extension rules.

0.41

Ensembl genome download and more sophisticated use of gene models (exons, introns, etc).

v0.40

v0.40 release, fix a memory over-use bug