History

This project extends covtobed, reimplementing the core algorithm in Nim.

• 2.7.0
  • bamtocounts now supports --paired to count fragments
  • bamtocounts fixed a bug that ignored the user flag to exclude
  • [EXPERIMENTAL] testing --extendRead INT in bamtocov #6
• 2.6.0
  • bamtocounts algorithm rewritten to accept unsorted and non-indexed files. the requirement for indexed files will be permanently dropped, for consistency across the suite, while we recommend using sorted files, and, in the future, this requirement might be added again to allow for performance gains.
• 2.5.0
  • BamToCounts rewritten with the target engine of BamToCov
• 2.4.0
  • Standed analysis is now supported with Wig-like output
• 2.3.0:
  • Improved Wig support
  • Improved GTF format detection
  • Expanded test suite
• 2.2.0:
  • Support for wiggle output (--wig STEP and --op FUNCT)
• 2.1.1:
  • Help screen for all the tools updated to reflect the new tool names
  • Added --tag STRING in bamcountrefs to customise the reference column name
  • Initial support for Wig files
  • Expanded test suite and memory/speed benchmarks
• 2.1.0:
  • Bug Fix: an assertion caused the program to fail if an alignment ended at the end of a chromosome.
  • Updated compilation instructions for Nimble and Bioconda builds
  • Speed improvements
• 2.0.4:
  • Added new internal classes, like output_t and coverage_t
• 2.0.2:
  • Added covtocounts
  • Added target support
  • Performance improvement
• 2.0.0:
  • Initial release: Nim porting of the original C++ code