Neoepiscope

Latest version: v0.7.0

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0.3.7

- Fixes bug in VCF processing to identify VAF field

0.3.6

- Adds functionality for a variety of new binding affinity prediction tools
- Adds transcript type, gene ID, gene name, and IEDB epitope identifier fields to output
- Removes necessity for `neoepiscope swap` mode (functionality retained)

0.3.5

- Updates haplotype processing to fix bug with complex indels
- Adds MANIFEST.in to address bug in PyPI installation

0.3.3

* Fixes bug that prevented processing of user-specified reference data for use in neoepitope predictions

0.3.2

* Adds processing step to break down haplotypes containing incompatible variants that are reported to be phased together

0.3.0

* Corrects previous variant phasing error by including homozygous variants in relevant haplotype blocks
* Corrects handling of intron-exon boundary deletions to truncate transcripts
* Corrects annotation of transcripts with start/stop codons split across multiple exons
* Expands functionality to allow for variant phasing using either HapCUT2 or GATK's ReadBackedPhasing
* Updates default gene annotation for _hg38_ to GENCODE v29
* Updates code for compatibility with intervaltree v3.0.2

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