pb-CpG-tools v3.0.0

v3.0.0 - 2025-01-27

Added

• CR-412 Add run metadata header to all bed output files

Changed

• CR-413 Compress and index all bed file outputs
• CR-411 Build default tflite model directly into binary
  • Users no longer need to provide a model file for the default model pileup mode
• CR-407 Release source code, update code to build in standard linux context

Fixed

• Improve error message when BAM index is missing

pb-CpG-tools v2.3.2

v2.3.2 - 2023-08-21

Fixed

• Improve error message when read length is too short for MM tag

pb-CpG-tools v2.3.1

v2.3.1 - 2023-05-10

Fixed

• Fix HP tag parse
  • The HP tag parser was not handling all possible binary int representations in BAM format
  • Fixes #47

pb-CpG-tools v2.3.0

v2.3.0 - 2023-05-02

Added

• Support alignment input in CRAM format

pb-CpG-tools v2.2.0

v2.2.0 - 2023-04-14

Added

• Added progress bar to bam processing step

Fixed

• Clarified error message when an unmapped alignment file is input

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Minor update to provide a progress meter for interactive (ie. tty) use. Options and file outputs are unchanged.

pb-CpG-tools v2.1.1

v2.1.1 - 2023-04-04

Fixed

• Fix parse error in MM/ML methylation tags
  • An infrequent error occurred when a reverse-mapped read ends (in sequenced orientation) with a C base annotated by the MM tag
  • Fixes #41

pb-CpG-tools v2.1.0

v2.1.0 - 2023-03-27

Initial update to the new binary version of aligned_bam_to_cpg_scores, replacing the similarly named python script
with a faster solution that should be simpler to install and run on linux systems. The new version has
near feature parity with the previous python script. See updated README contents for details.

v1.1.0

Includes several new features and addresses previously reported bugs.

v1.0.0

Initial release.