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NEWS.md

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Version 1.8.0

  • Fixed parsing of reads containing insertions (closes #104)
  • Fixed handling of gzip and bzip output files and filenames
  • Remove support for Python 2.7. It may still work, but I'm no longer going to try to maintain compatability with both Python 2 and 3.

Version 1.7.0

  • Fixed parsing of --methylation-type argument (closes #102)

Version 1.5.4

methtuple now requires pysam v0.8.4 or greater. methtuple now support Python 3.5.

Bug fixes

  • Fixed failing tests due to changes between pysam v0.8.3 and v0.8.4.

Internal

  • methtuple now requires pysam v0.8.4 or greater

Version 1.5.3

methtuple now requires pysam v0.8.3 or greater.

Bug fixes

  • Fixed failing tests due to changes between pysam v0.8.2 and v0.8.3.

Internal

  • methtuple now requires pysam v0.8.3 or greater

Version 1.5.0

methtuple now requires pysam v0.8.1 or greater.

Bug fixes

  • Fixed Python 3 compatibility issues due to changes in the pysam API (closes #94).

Internal

Moved to the new pysam API. As a result, methtuple now requires pysam v0.8.1 or greater.

Version 1.4.0

This version of the software changes the name from comethylation to methtuple to better reflect what it actually does.

I have also switched to the MIT licence.

New or improved features

  • Added --all-combinations option to create all possible m-tuples including non-neighbouring ones. This will greatly increase the memory usage if combined with larger values of --m (e.g. > 2).

Version 1.3.0

New or improved features

  • Support reads containing indels (closes #25 and #45).
  • Refined process for dealing with overlapping reads (closes #15).
  • Improved documentation (closes #82 and #84).
  • Python 3.4 support.

Minor improvements

  • Added NEWS file.

Bug fixes

  • Provide default --ir1p and --ir2p (closes #79).
  • Switched to *nix style line endings (\n), rather than the Windows line endings (\r\n), for the .tsv file (closes #83).
  • Switched back to samtools instead of Picard in helper_scipts/run_comethylation.sh (closes #78).
  • Updated examples to use Bismark v0.12.5.

Internal

  • Simplified creation of m-tuples.
  • Added get_positions function to get the reference positions of all bases in a read (including None if no reference base, such as inserted bases or soft-clipped read-positions).
  • Added process_overlap function to process overlapping paired-end reads using the given --overlap-check

:(

  • Running time of v1.3 is 2-3x slower than v1.2. Partly because reads with indels are no longer skipped and partly because of code simplifications. Should be able to improve performance now that some internals have been simplified.

Version 1.2.0

New or improved features

  • Python 3 support (not yet Python 3.4 compatible due to limitations of current version of Pysam).
  • Include strand of m-tuple in output.

Minor improvements

  • Updated examples to use Bismark v0.12.2 (closes #65).
  • Update data/run_comethylation.sh to use command line interface introduced in v1.1.
  • Improved filtering of specific read-positions.

Bug fixes

  • Fixed bug that meant the sum of the overlap scores was incorrect for paired-end reads aligned to the OT-strand.

Version 1.1.0

New or improved features

  • Complete re-design and simplification of command line interface (closes #74)
  • Reduced memory usage (addresses #64).
  • Added support for gzip and bzip2 output files (closes #69).
  • Added parallelisation via GNU parallel in helper_scripts/run_comethylation.sh(closes #68).
  • Ignore specific read-positions rather than just start or end (closes #71)

Bug fixes

  • --methylationType CHG requires --strandSpecific (closes #72).

Internal

  • Refactored WithinFragmentComethylationMTuple class as part of memory usage improvements.

Version 1.0.0

Initial public release