20.7.1

Updates to project structure and documentation for PyPi release.

Features:

• New user documentation available on readthedocs
• Now pip-installable from PyPi
• New command line usage by directly using VaSeBuilder after installing with pip

20.06.1

Major updates:

• new command line interface using argparse
• option to disable context merging
• option to disable sample ID hashing
• variant loci per context are now written to varcon output files
• New customizable inclusion filters and prioritizations

Minor updates:

• added integration testing files
  • pylint, Jenkins, pythonapp.yml, etc.
• added requirements.txt for pip
• updates to comparison tool Ygor
• linting
• deprecated file cleanup

19.10.1

Major updates:

• All AC and F mode donor reads are distributed equally across all acceptor FastQ files.
• AC and F mode now insert donor reads into random positions across acceptor FastQs.
  • (Donor R1's and R2's are inserted into the same positions in their respective files.)
• Variant context window end positions now determined by the last aligned base, instead of the alignment start + read length.
  • More consistent with how start position is determined.
• Hardclipped secondary alignment sequences are replaced with their primary (unclipped) sequences.
• Random seed parameter added to replicate runs.
• Added more documentation.
  • Input / output format documentation in "docs" folder.
  • NumPy-style docstrings for methods.

Other changes:

• Mate fetching bug fixed, no longer possible for a read to fetch itself by accident.
• Build_varcon_set methods now split into smaller chunks.
• Runmode methods split into individual functions.
• New P-mode link (PLink) file tracks donor FastQ filenames produced per variant.
• New random seed parameter allows user to replicate the semi-random read distribution between runs of the same data.
• New donor insert position output file lists FastQ read positions of each inserted donor read.
  • Ex. If donor read "readABC" is added after the 100th acceptor read in the FastQ, the output file will list "readABC" as being inserted at position 101 (corresponding to FastQ lines 405 - 408).
• VaSeBuilder UUID for each run is now added to each output file for run tracking.

19.08.1

New features:

• Addition of mode flags:

  • FastQ output modes:
    • "F" (default): Outputs full validation set of combined acceptor and donor reads
    • "A": Combines pre-existing FastQ donor files with filtered acceptor reads (requires pre-existing variant context file)
    • "D": Outputs combined donor reads only
    • "P": Outputs individual FastQ files per variant
    • "X": No FastQ output
  • Variant context modes:
    • No option specified (default): Builds a variant context file from inputs
    • "C": Accepts a pre-existing variant context file to build FastQ files from

• Restructured variant context building and FastQ writing

• Added support for input of configuration files with preset argument parameters

• "A" mode donor FastQ files are distributed across acceptor FastQ files

Future plans:

• May implement distribution of individual donor FastQ reads across validation set FastQ output files, instead of distributing whole FastQ files
• Parellelization of FastQ writing
• Variant context file checks, to ensure that user-created variant context files do not contain overlapping contexts

19.07.1

Second release. New features:

• List-based donor file input.
• Donor variant filtering based on an optional inclusion list.
• CRAM support.

19.06.1

Initial release.