v1.2.0b1

What's Changed

• Fix invalid escape sequence warning message by @bepoli in #19
• Set multiple verbosity level by @bepoli in #21
• Converge multi-mapped UMIs estimates with tolerance threshold of log-likelihood change between EM iterations by @bepoli in #20

Full Changelog: v1.1.2...v1.2.0b1

v1.1.2

What's Changed

• Enhance compatibility with different versions of python (PR: #18)
  • Fix bug causing incompatibility with python 3.8 (a8a4549)
  • Remove support for python 3.7 (f379595)

Full Changelog: v1.1.1...v1.1.2

v1.1.1

New release to force sync with Zenodo. Equivalent to v1.1.0 release.

v1.1.0

What's Changed

• Add option "--dumpEC" to write a log table with Equivalence Classes and UMI mismatch corrections (PR: #13)
• Add options --min-bp-overlap and --min-fraction-overlap to set a minimum overlap between read and TE (PR: #14)
• Merge 1.1.0-beta.2 (PR: #16)
  • Improve the TE-UMI deduplication by using directed graphs (inspired by umi-tools directional algorithm).
  • Use networkx to handle graphs.
  • Make the EM procedure compatible with the new deduplication strategy.
  • Make EM operations on a numpy matrix to increase performance.
• Minor adjustments to docs and syntax (PR: #17)

Full Changelog: v1.0.3...v1.1.0

v1.1.0-beta.2

What's Changed

• Improve the TE-UMI deduplication by using directed graphs (inspired by umi-tools directional algorithm).
• Use networkx to handle graphs.
• Make the EM procedure compatible with the new deduplication strategy.
• Make EM operations on a numpy matrix to increase performance.

Full Changelog: v1.1.0-beta.1...v1.1.0-beta.2

IRescue version v1.1.0-beta.1

Enhancements

• Add option "--dumpEC" to write a log table with Equivalence Classes and UMI mismatch corrections (PR: #13)
• Add options --min-bp-overlap and --min-fraction-overlap to set a minimum overlap between read and TE (PR: #14)

Full Changelog: v1.0.3...v1.1.0

IRescue version 1.0.3

Bug fixes

• Fix bug causing few barcodes missing from matrix when using multiple cpus (PR: #7)
• Skip BAM lines without the chosen cell barcode tag (for increased compatibility with Cell Ranger BAM files) (PR: #11)
• Fix bug causing not deduplicating UMIs when some UMI graph configurations occur (PR: #12)

Enhancements

• Add tests (PR: #6)
• Skip multiprocessing when using 1 cpu (should make preprocessing slightly faster) (PR: #5)
• Skip chr if not in rmsk (as above) (PR: #8)
• Better error handling: provide better error description in various situations, such as those described in #1 (PR: #10)

Full Changelog: v1.0.2...v1.0.3

IRescue version 1.0.2

• bugfix: allow the presence of /1 or /2 at the end of read names (closes #1)
• bugfix: allow for more generic naming of TE features in the 4th column of the bed input file (closes #1)

Full Changelog: v1.0.1...v1.0.2

IRescue version 1.0.1

• Add usage and description in --help

IRescue version 1.0.0

Initial release