MiModD

Fix symlinks by specifying relative targets

Add more tests for variant_annotation module

fixed by [2482ec]

Reverse-complement EFF allele when reverting ALT during rebase

mimodd reheader bug with renaming ref sequences in BAM

correction to the correction: the real cause of the issue is that the SnpEff effect allele (which SnpEff writes correctly in every case) can get out of sync with the ALT column during rebasing (which may rv-complement ALT alleles, but doesn't know about SnpEff effects fields).

fix wrong alleles in variant reports

variant call tool should expose more samtools/bcftools options

Merge Snap and vcf-filter fixes into stable

allow unspecified start or stop in vcf-filter region filters