6.0.1

What's Changed

• bumps version of gtfparse by @chrisamiller in #96

Full Changelog: v6.0.0...v6.0.1

6.0.0

What's Changed

• Gzip by @chrisamiller in #86
• Multiinfo by @chrisamiller in #87
• Adding the ability to extract additional bam-readcount fields into the by @chrisamiller in #85
• Update vcfpy dependency to a newer version by @susannasiebert in #84
• encoding issues in files merged from another PR by @chrisamiller in #90
• vcf-expression-annotator updates by @chrisamiller in #92
• adding contribution policy by @chrisamiller in #93
• updating docs by @chrisamiller in #88
• upgrading to vcfpy 0.14.2, dropping support for python 3.8, 3.9 by @chrisamiller in #91
• adding tx/gx file input type warnings for stringtie by @chrisamiller in #94
• Docs2 by @chrisamiller in #95

Full Changelog: v5.2.0...v6.0.0

5.2.0

What's Changed

• Refactor vcf-expression-annotator to be faster by @susannasiebert in #79
• Allow vep annotation reporter to provide a list of preferred transcripts by @susannasiebert in #81

Full Changelog: v5.1.1...v5.2.0

5.1.1

What's Changed

• Update ref transcript mismatch reporter to handle protein coding variants by @susannasiebert in #75

Full Changelog: v5.1.0...v5.1.1

5.1.0

What's Changed

• fixing typo by @chrisamiller in #54
• Update tests to run in newer Python versions by @susannasiebert in #64
• Update the expression annotator to use the gene (ID) column in Kallisto files by @susannasiebert in #66
• Update vcf-expression-annotator documentation to clarify custom id-column parameter by @susannasiebert in #67
• Prevent ZeroDivisionError errors in log output by @susannasiebert in #68
• Handle case in the ref-transcript-mismatch-reporter where there is no protein position annotation by @susannasiebert in #69
• Output warning when VCF is annotated with the PICK flag but not transcript was PICK'ed by @susannasiebert in #70
• Downgrade duplicate variant error to a warning and skip duplicates. by @susannasiebert in #71
• Add per-strand allele counts when running vcf-readcount-annotator by @susannasiebert in #72

Full Changelog: v5.0.1...v5.1.0

5.0.1

What's Changed

• Move tests to GitHub actions by @susannasiebert in #51
• Handle stop_retained_variant, * in wildtype protein sequence, and protein position edge cases by @susannasiebert in #50

Full Changelog: v5.0.0...v5.0.1

5.0.0

What's Changed

• Fix warning message for the VCF expression annotator when running in gene mode by @susannasiebert in #45
• New tool ref-transcript-mismatch-reporter by @susannasiebert in #44

Full Changelog: v4.1.0...v5.0.0

4.1.0

What's Changed

• Fix bug with vcf-genotype-annotator that would fail when trying to add a dummy sample to VCFs with existing samples by @susannasiebert in #40
• Add support for adding genotype to an existing single-sample VCF by @susannasiebert in #41

Full Changelog: v4.0.0...v4.1.0

4.0.0

What's Changed

• Add new tool transform-split-values by @susannasiebert in #21
• Allow --ignore-transcript-version argument to also work on gene identifiers by @susannasiebert in #29
• New tool to add new samples with genotype fields to a VCF by @susannasiebert in #33

Full Changelog: v3.1.0...v4.0.0

3.1.0

What's Changed

• clarify input format by @chrisamiller in #24
• join multiple transcripts with a comma by @apaul7 in #26

New Contributors

• @apaul7 made their first contribution in #26

Full Changelog: v3.0.1...v3.1.0