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Commits on Jul 26, 2020

• Handle exception raised when input file has no structural variants.

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Commits on May 20, 2020

• Remove temp files

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• Reprocess annotation based on notes

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Commits on May 19, 2020

• use production vep

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Commits on May 18, 2020

• removed useless module

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• Multiple changes concerning batch processing

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Commits on May 14, 2020

• Updates to exception handling in the main function.

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• Format change to ote string

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Commits on May 11, 2020

• Use tmpdir for temp out files

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Commits on Dec 11, 2019

• ongoing changes for enabling batch processing

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• linting

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• Look for the last element in the site description list to get exon number

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• Changes to VEP parameters, particularly buffer-size and forks, for efficiency

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• include FASTA file path

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• :zap: adding a config module that includes file paths as constants

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• :zap:

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Commits on Dec 9, 2019

• :zap: Enable multiprocessing. TODO: add logging

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• linting

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Commits on Dec 6, 2019

• GUCD1 added

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• Update transcript ID for GUCD1 and MBD3

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Commits on Feb 28, 2019

• update description

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• enable annotations for intragenic deletion with both breakpoints in the same intron

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Commits on Feb 27, 2019

• use rootdir to get path for data files

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Commits on Feb 26, 2019

• update README

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• remove notes_constants

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• add test data

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• add data sources

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• update README

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• validated version of the notes module for Feb 2019 release

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• add 5 seconds timeout for vep API query

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• Exclude JAK and LATS genes from kinase annotation. Also convert hotspot and tumoursuppressor to list

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• fix translocation annotation

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• fix IKZF1

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Commits on Feb 25, 2019

• bugfix for EGFR vIII

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• add ensembl lookup transcript for PRIM2. Refseeq canonical NM_000947.5 is not included in vep

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