IsoQuant 3.4.0

Major novelties and improvements:

• Significant speed-up on datasets containing regions with extremely high coverage,often encountered on mitochondrial chromosomes (#97).

• Added support for Illumina reads for spliced alignment correction (thanks to @rkpfeil).

• Added support YAML files (thanks to @rkpfeil). Old options --bam_list and --fastq_list are still availble, but deprecated since this version.

Transcript discovery and GTF processing:

• Fixed missing genes in extended GTF (#140, #147, #151, #175).

• Fixed strand detection and output of transcripts with . strand (#107).

• Added --report_canonical and --polya_requirement options that allows to control level of filtering of output transcripts based on canonical splice sites and the presence of poly-A tails. (#128).

• Added check for input GTFs (#155).

• Extract CDS, other features and attributes from reference GTF to the output GTFs (#176).

• Reworked novel gene merging procedure (#164).

• Revamped algorithm for assigning reads to novel transcripts and their quantification (#127).

Read assignment and quantification:

• Optimized read-to-isoform assignment algorithm.

• Added gene_assignment_type attribute to read assignments.

• Fixed duplicated records in read_assignments.tsv (#168).

• Improved gene and transcript quantification. Only unique assignments are now used for transcript quantification.
  Added more options for quantification strategies (--gene_quantification and --transcript_quantification).

• New option to control TPM computing (--normalization_method).

• Improved consistency between trascript_counts.tsv and transcript_model_counts.tsv (#137).

• Introduced mapping quality filtering: --min_mapq, --inconsistent_mapq_cutoff and --simple_alignments_mapq_cutoff (#110).

Minor fixes and improvements:

• Added --bam_tags option to import additional information from BAM files to read assignments output.

• Large output files are now gzipped by default, --no_gzip can be used to keep uncompressed output (#154).

• BAM stats are now printed to the log (#139).

• Various minor fixes and requests: #106, #141, #143, #146, #179.

Special acknowledgement to @almiheenko for testing and reviewing PRs, and to @alexandrutomescu for supporting the project.