Version 0.11

pipette 0.11.0 (2023-07-13)

Major changes:

• Now requiring R 4.3 / Bioconductor 3.17.
• File classes for import and export are now prefixed with Pipette, to avoid unwanted collisions with other classes defined in Bioconductor packages.
• import: Added support for MAF files.
• import: Added support for BAM, CRAM, and SAM files. Note that CRAM files must be able to resolve the corresponding reference genome.
• import: Added support for BCF and VCF files. Note that these files currently require corresponding CSI index files, which can be generated using htslib.
• Temporary files generated during import calls (i.e. automatic decompression of compressed files, such as gz or xz) are now automatically cleaned up. This change should only affect temporary files. If you notice any issues with this, please file a bug report!
• getJSON: Reworked to use httr2 instead of deprecated httr package.

pipette 0.11.1 (2023-07-27)

Minor changes:

• getJSON: Improved code coverage for parsing of Ensembl REST API.

pipette 0.11.2 (2023-08-12)

Minor changes:

• import: Disabled lazy loading mode for readr. Enabling this makes it basically impossible to suppress warnings when parsing malformed files, such as in the MGI function of AcidGenomes.
• Enabled parallel testthat unit tests.