Commits

Author Commit Message Labels Comments Date
Sean Davis
Added some random scripts as dumping ground
Sean Davis
Added sample genotype output option to vcf melt
Sean Davis
Switched from Levenshtein to pylev--probably slower, but at least builds
Sean Davis
Working on maf to vcf conversion
Sean Davis
Added dist to .gitignore
Sean Davis
Temporarily remove python-levenshtein dependency (no python3 support)
Sean Davis
Added non-working delly.py
Sean Davis
Fix issue #2
Sean Davis
Changed over to MIT license
Sean Davis
Added GPL licensing
Sean Davis
Fixed encoding issues associated with richly-annotated vcf files (some bad bytes)
Sean Davis
Removed stray print statement in strelka fixer
Sean Davis
Using python3 gzip for incredible performance improvements over subprocess gzip
Sean Davis
Fixed fastq IO reading to account for python3 changes
Sean Davis
Added rnacount functionality
Sean Davis
Version bump
Tags
0.3.4
Sean Davis
Since PyVCF is splitting on commas in info fields, we need to put them back together when they are not specifically labeled as an array (num>1)
Sean Davis
Looks like PyVCF splits on commas, now, so the snpEff effects are already a list
Sean Davis
Had left func() definition out for meltVcf--fixes "namespace" has no attribute "func"
Sean Davis
Fixed strelka to use only tier 1 counts, per Chris Saunders recommendation
Sean Davis
Added strelka processing to vcf subcommand
Sean Davis
VCF melt now splits array fields into separate columns
Sean Davis
Version bump in docs
Sean Davis
version bump
Sean Davis
Python3 compatible and small bug fix in dealing with "CUSTOM" snpEff tags in vcf melt
Sean Davis
Added ability to add samplename to vcf melt text file
Sean Davis
Partial change to demultiplexer to use levenshtein distance to match indexes
Sean Davis
Added link in documention to bitbucket
Sean Davis
Added PyVCF as a dependency.
Sean Davis
Removed a couple stray print statements from vcfMelt
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