Multi-threading;
Intermediate results are saved to disc to enable quick restart via --read_assignments option;
Significantly improved precision for novel transcript detection;
Secondary alignments are now used by default;
Fixed several bugs in inconsistency detection algorithm;
Reworked polyA detection and reporting once again;
Slightly modified read assignment output format;
More informative GTF output;
Removed --has_polya option, --polya_trimmed is now used as the opposite;
Added --check_canonical option.
Significantly reworked polyA detection and reporting;
Improved detection of inconsistencies, added several new event types;
Better recall and precision for read assignment algorithm;
Fixed several bug and flaws;
Added script for counting simple stats for GTF files (srt/gtf_stats.py).
Initial release.