New options for controlling quantification strategies. Default behaviour is changed as well.
New option --genedb_output for providing a separate folder for gene database in case the
output directory is located on a shared disk.
Possibility to provide read group tables in gzipped format.
Fixed --check_canonical option.
Improved running time for the read assignment step (noticeable only for genes with > 100 exons).
Minor fixes and improvement in output files. Note, that GTFs and some other files have now multiline headers.
Parallel processing of transcript model construction phase.
Minor improvements in quantification of reference transcripts.
Fixed counts/TPM for novel transcript models.
Fixed processing of BAM records without sequence data (e.g. secondary alignment).
Fixed list index out of range bug in long read counter.
Improved recall by introducing relative coverage cutoffs.
More careful handling of transcript terminal positions.
Fixed GTF to BED conversion.
Completely new transcript discovery algorithm with significantly higher recall.
Algorithm for read alignment correction.
Support for technical replicas within a single sample.
Significantly improved running time and RAM consumption;
Annotation is now fed into minimap2;
Extended output format.
Support for GFF3 mRNA features.
Support for BAM files with =/X in CIGAR strings;
Fixed canonical splice site detection.
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.