0.6.0

Code Refactoring:

• Improved code structure, readability and the documentation
• Fixed consistency between counts and read info table
• Improved test coverage by adding more unit and integration tests

Bug fixes:

• Fixed bug where bowtie2 multi-mappers were not properly counted as junction and spanning reads

Other:

• Improved and updated README
• Added snp_or_indel info into read info table

Full Changelog: 0.5.5...0.6.0

0.5.5

Release notes:

• Fixed secondary alignment output in bowtie2
• Added custom parameters for bowtie2
• Remove discordant reads from bowtie2 alignment
• Removed bwa from alignment tools
• Added option to omit singletons from re-quantification
• Added sanity checks for alignment files
• Added the following information to read info table:
  • flag
  • bp
  • cigar
  • total_mismatches
• Implemented an improved mode for quantification to reduce memory footprint
• Added Docker manifest

Known issue: Junctions reads that overlap the end of context-sequences are not properly counted

Full Changelog: 0.5.4...0.5.5

0.5.4

• Updated bowtie2 version to 2.5.3 in environment to fix segmentation fault
• Fixed counting issue for secondary alignments while using bowtie2

0.5.3

• Fixed BAM flag filter to not discard secondary alignments
• Updated bowtie2 alignment parameters to include multimapper and perform end-to-end alignments
• Fixed calculation of library size
• Add test sequences to test multimapping reads

0.5.1

• Added mismatches to read info output table
• Fixed bug in plotting script

0.5.0

• Created Python package
• Added cleanup step

0.4.2

• Updated requantification to also consider junction reads for pairs of which the second read is unmapped (affects only STAR mapping)
• Unmapped reads are now included in BAM file
• Adjusted counting scheme for singleton junction reads

0.4.1

• Added compatibility for BAM file input
• Added custom STAR parameters as commandline argument
• Added input read count file to output results

0.4.0

• Added intron retention detection using interval-mode and coverage output
• Added option to choose between different aligners (bowtie2, bwa and STAR)
• Added some configurable parameters to tune alignment output
• Removed unused code and made code more compact
• Reduced memory consumption during requantification step

0.3.6

• remove unused bash scripts
• update default config
• update README with GitHub-based install instructions