Version 1.3.0

Data Created:

• 13 November 2024

General Notes:

• Moved README documentation to website: https://huishenlab.github.io/dupsifter/

Updated Features:

• Barcode option enabled for single-end data. Added by koriege.
• N's can now be included in the barcode string. Added by koriege.

Compilation Information for Pre-Compiled Binaries:

• Linux version:
  • OS: Alma Linux version 9.4
  • GCC: gcc (GCC) 11.4.1 20231218 (Red Hat 11.4.1-3)
  • CPU: Intel Xeon x86_64
• macOS version:
  • OS: Sonoma version 14.6.1
  • GCC: Apple clang version 15.0.0 (clang-1500.3.9.4))
  • CPU: Intel Xeon

Version 1.2.1

Data Created:

• 19 January 2024

General Notes:

• Added bioconda install to README.

Bug Fixes:

• Issue #1 fixed (extended CIGAR operations not included when inferring bisulfite strand). Reported by koriege.

Compilation Information for Pre-Compiled Binaries:

• Linux version:
  • OS: Alma Linux version 9.2
  • GCC: gcc (GCC) 11.3.1 20221121 (Red Hat 11.3.1-4)
  • CPU: Intel Xeon x86_64
• macOS version:
  • OS: Monterey version 12.7.2
  • GCC: Apple clang version 14.0.0 (clang-1400.0.29.202)
  • CPU: Intel Xeon

Version 1.2.0

Data Created:

• 26 September 2023

General Notes:

• Print reference file path when running in verbose mode.
• Add check for file extension of reference FASTA.
• Modify output for time after running dupsifter
• Print inferred bisulfite strand when running in verbose mode.
• Add library dependencies to README.
• Create docker container
  • Dockerfile provided in container directory will build with the latest release version of dupsifter.
  • Dockerhub version available (see README for details on pulling from Dockerhub).
  • Can also use Singularity to pull container from Dockerhub.
  • Python script available to create container file for specific version.
• Add walkthrough in example directory.
  • Includes FASTQ files and BAM files aligned with different WGBS aligners to test running dupsifter.

Compilation Information for Pre-Compiled Binaries:

• Linux version:
  • OS: Alma Linux version 9.2
  • GCC: gcc (GCC) 11.3.1 20221121 (Red Hat 11.3.1-4)
  • CPU: Intel Xeon x86_64
• macOS version:
  • OS: Monterey version 12.6.9
  • GCC: Apple clang version 14.0.0 (clang-1400.0.29.202)
  • CPU: Intel Xeon

Version 1.1.1

Data Created:

• 15 June 2023

General Notes:

• Clean up #include header files to be in better locations.
• Rework DEBUG / WARNING / ERROR messages to have a more consistent format.
• Update README.

Updated Features:

• Revised how the barcode is included in the signature.
  • Previously, it was extracted from the read itself, but leaving the barcode in the read would impact alignments. Now, the barcode is pulled from either the CB SAM tag, the CR SAM tag, or parsed from the read name.

Version 1.1.0

Data Created:

• 8 June 2023

General Notes:

• Update copyright.
• Add --version option to help message.
• Remove unused libraries in Makefile.
• Resolve gcc compiler warnings.

New Features:

• A barcode / UMI can now be used in the signature. At this time, it only works for barcodes / UMIs that have not been removed from the BAM SEQ string, but the goal will be to expand this to include strings found in the read ID or in SAM auxiliary tags.

Bug Fixes:

• Remove config state from help message. Generally, the config provided correct default values, but not always.

Version 1.0.0

Date Created:

• 4 August 2022

General Notes:

• Version used for publication comparisons
• Uses HTSlib version 1.15.1
• All dependencies included, no extra installations required