v1.4.0 (2024-04-14)

Added meta_min_reads parameter to control minimum coverage for metagene plots (#155)
Formatting changes

v1.3.3 (2022-02-09)

Print start codons when preparing orfs
Fix for custom start codons

v1.3.2 (2020-05-03)

Better support for extracting sequences from non-conventional GTFs
Support --protein flag for extracting protein sequences

v1.3.1 (2019-12-12)

Detecting uniquely mapping reads now raises a warning instead of aborting. We expect the user to ensure all reads in the bam are uniquely mapping unless it was produced for aligners that support either the NH or standard uniquely mapping flags (See common.py for a list of flags).
Clean setup.py to improve classifiers

v1.3.0 (2019-11-01)

A small bug fix in metagene.py where the first annotated CDS was being skipped
Silenced progress bars after they are complete
More informative progress messages

v1.2.0 (2019-10-09)

Added additional flags for filtering:
- --min_valid_codons_ratio (default=0): Minimum ratio of codons with non-zero reads to total codons for determining active translation
- --min_reads_per_codon (default=0): Minimum number of reads per codon for determining active translation
- --min_read_density (default=0.0): Minimum read density (total_reads/length) over an ORF total codons for determining active translation
Added a new command-line argument to learn dataset-specific parameters from Ribo-seq and RNA-seq bams learn-cutoff
Travis based CI testing

v1.1.0 (2019-09-17)

Allow specifying custom phase score cutoffs
Added documentation for species-specific cutoffs
Helper functions for determining best cutoff given golden datasets

v0.1.0 (2019-05-05)

First release of ribotricer on pypi