v1.1.3

• We have modified the instructions for utilising Docker/Singularity with InDelible in response to several issues (#9, #13)
• We have made hg38 resource files easier to use with Docker/Singularity
• We have added test data for hg38 to the repository
• Increased the default version of PyMAL to v5.4 due to a security issue (#11)
• Created more stable instructions for installing InDelible Python package requirements and various improvements to the README for clarity (#10)
• Made various small code updates to make InDelible compatible with Pythonv3.8
• Fixed a bug when --keeptmp is not used during complete that would try to delete nonexistant files

v1.1.2

Post release bug fixes and feature requests.

• Made various fixes/feature additions for when using priors (issue #8):
  • Fixed a bug that was related to an accidentally hardcoded path and differences in the newest version of pandas. Please update your version of pandas if you encounter bugs/errors when running the 'Database' subcommand of InDelible.
  • Added a flag to the database and complete commands (--old-maf) which tells InDelible to use the MAF information in the provided priors file for identical loci rather than from the sample(s) provided by the user.
  • Fixed an error in the readme that claimed the priors file had 12 instead of 14 columns.

v1.1.1

1.1.1 - Minor bug fixes and finalizing implementation of the new "database" module

• See issue #4 for more information on "database" fixes
• Updated the data.zip files (both hg19 and hg38) to include data that is compatible with the new "database" module
  • If using hg38, please read the caveats in the "Installation" section of the README
• Fixed issue relating to decoy chromosomes with underscores ("_") were causing InDelible to break
• Removed the pybedtools dependency. Users were experiencing issues where bedtools would only generate a coverage graph for the very beginning of a cram/bam file and then die without sending an error. InDelible now directly calls bedtools.
  • PLEASE NOTE: bedtools is still required to be installed and in your PATH for indelible to run.

v1.1.0

1.1.0 – Bug fixes and new functionality

This release results in incompatibility between v1.0.0 and v1.1.0 at some stages of the InDelible pipeline.

• All step's outputs prior to "Database" are compatible.
• We have removed the "Blast" module from the InDelible pipeline. All functionality previously performed by this module has been placed within the "database" module. As such, database is now a required step in the InDelible SV calling pipeline. Please see database for more information.
  • Alongside this change, we have added additional functionality for determining SV types (i.e. DEL/DUP/INS/etc) and breakpoint information. Please see output for more information.
  • These changes have also required us to modify where InDelible filters sites based on our active learning approach in the score step. This change means that the output of annotate will only contain breakpoints that pass the SCORE_THRESHOLD as defined in the provided config.yml file (default is sites with probability >= 0.6). As a reminder, all raw variants are still available in the output of score.
• We have removed several columns from the previous InDelible primary output from "denovo". These primarily relate to how InDelible handles the removal of the "blast" step and has switched to using bwa mem for this functionality.

v1.0.0

1.0.0 – Initial InDelible release

This release was generated concurrently with the publication of our medRxiv manuscript detailing InDelible.