griffithlab/pVACtools: 3.0.1

This is a bugfix release. It fixes the following problem(s): There was small issue in pVACview where picking a different number of variants in the main table would cause changes to variant evaluations to not be recorded correctly. This release also fixes a problem where loading a new set of files into pVACview would not reset previous evaluation summary counts. This release fixes an error in pVACtools that would occur when a chromosomal region in the somatic VCF is not present in the proximal VCF. This release adds further error checking for malformed CSQ header descriptions. This release updates various code portions to remove deprecation warnings and add support for newer versions of certain dependencies (e.g. pandas). This release fixes an bug with the standalone pvacseq calculate_reference_proteome_similarity command where picking a custom --match-length would throw an error. Some users were reporting errors during the tmp file cleanup stages of running the various pipelines. This releases fixes that issue