Pvactools

This is a bugfix release. It fixes the following problem(s):

- The previous version updated how the all_epitopes.tsv file was parsed when creating the aggregated report and NA values are now parsed as native pandas nan. However, this update was not handled correctly for the Mutation Position column, leading to errors with NA values in that column. This release fixes this error. ([1079](https://github.com/griffithlab/pVACtools/pull/1079))
- The previous version would write the DeepImmuno output file in the same location for multiple prediction calls. This would lead to errors when running in multi-threaded mode. This releases updates the code to write DeepImmuno outputs to unique file locations. ([1078](https://github.com/griffithlab/pVACtools/pull/1078))
- This release updates how the list of combinatorial class II alleles is created in order to return it as a sorted list, creating a consistent order when writing the input.yml log file. ([1077](https://github.com/griffithlab/pVACtools/pull/1077))
- This release updates the GitHub commit for the pVACview demo data in order to pull the latest version of this data, including DeepImmuno and BigMHC prediction data. ([1073](https://github.com/griffithlab/pVACtools/pull/1073))
- This release fixes an issue where the pVACvector visualization images were saved in a low resolution format resulting in blurry images. ([1071](https://github.com/griffithlab/pVACtools/pull/1071))
- This release fixes an issue where the method to determine the matched wildtype result didn’t return where appropriate, causing the mutation position to not be set correctly. ([1082](https://github.com/griffithlab/pVACtools/pull/1082))
- This release fixes some typos. ([1072](https://github.com/griffithlab/pVACtools/pull/1072))

This is a minor feature release. It adds the following features:

- This release adds support for two new prediction algorithms: BigMHC and DeepImmuno ([1063](https://github.com/griffithlab/pVACtools/pull/1063)). BigMHC includes predictions for elution (BigMHC_EL) and immunogenicity (BigMHC_IM). DeepImmuno is a prediction algorithms for immunogenicty.
- This release includes several updates to pVACview ([1012](https://github.com/griffithlab/pVACtools/pull/1012)):
- The tab containing the anchor heatmaps for each well-binding peptide of a variant has been moved to the “Transcript and Peptide Set Data” panel.
- The anchor heatmap tab now also contains a table of all the per-length and per-allele anchor weights for each position in a peptide.
- The pVACtools version is now displayed at the bottom of the sidebar.
- A new panel has been added to show the tiering parameters currently applied.
- Where there are multiple transcript sets for a variant, the one containing the best peptide is now selected by default.

- This release adds a new command pvactools download_wdls ([1055](https://github.com/griffithlab/pVACtools/pull/1055)). This command can be used to download WDL workflow files for pVACseq and pVACfuse.

This is a bugfix release. It fixes the following problem(s):

- pVACbind was not parsing the individual El prediction algorithm scores correctly resulting in them being missing from the all epitopes file.
- This release fixes some display issues in pVACview. It also implements a Docker file and bash script for deploying pVACview to GCP.

This is a bugfix release. It fixes the following problem(s):

- The multithreading capabilities in pVACtools are not available for Mac OSX. Attempting to use the -t parameter would result in the forked processes crashing but the run would still complete successfully leading to results with incomplete data. This release will result in an error when multithreading is used under Mac OSX.
- We’ve observed issues with IEDB’s API sometimes returning incorrect or incomplete data. This results in downstream errors. This release updates the prediction calling to log such occurrences and to retry the API when they are observed.
- MHCflurry sometimes returns no binding affinity percentile data. This resulted in errors when parsing such prediction data. This release fixes our parsing logic to handle this case.
- TSL parsing of the input VCF in pVACseq used to be limited to human data only. This release adds support for TSL parsing in mouse data.
- When running with the –noncanonical flag, the exons.csv file will contain exon postions for all possible transcript combinations. However, the transcripts weren’t being taken into account when parsing this file to determine the fusion positions. This release fixes this issue by looking up the positions for the specific transcripts of the record currently being parsed.
- When using BLASTp for the reference proteome match step, we applied the word-size parameter in order to only return perfect matches. However, for short sequences, word-size must be less than half the query length, or reliable hits can be missed. This release updates how the word-size parameter is calculated in order to meet this criteria.
- This release addresses in error in pVACview that would occur in the Transcripts in Set window when there are no peptides passing the aggregate inclusion binding threshold.

This is a bugfix release. It fixes the following problem(s):
- A bug in the aggregate report creation incorrectly evaluated the Transcript Support Level and resulted in picking the wrong Best Transcript in some cases.

This is a bugfix release. It fixes the following problem(s):

- In recent releases, users have noticed that at some point during pipeline runs, predictions to MHCflurry would hang or get killed. We were able to determine that the cause was related to [PR 988](https://github.com/griffithlab/pVACtools/pull/988). This PR originally updated calls to MHCflurry to happen by instantiating their predictor within Python instead of calling it on the command line. However, we suspect that this causes a substantial increase in memory usage resulting in the observed behavior. This release reverts the change from PR 988.