v0.2.6

v0.2.6 Fix allele finding problem with uppercasing strings

v0.2.5

v0.2.5: handle input VCFs with differing cases in REF and ALT alleles

Avoids issues when some input VCFs have lower versus uppercase in allele
representations. Consistently convert to upper case for preparation and
comparisons.

Fixes #2924
Fixes #2350

v0.2.4

v0.2.4: platypus fix for contig VCF headers

Ensure Platypus output files have contigs in the VCF header, which
avoids downstream errors with GATK4 GatherVcfs.
bcbio/bcbio-nextgen#2688

v0.2.3

v0.2.3: fix wrapper script to correctly check for JAVA_HOME

Fixes #22

v0.2.2

v0.2.2: support for recent bcftools; improved logging

- Handles issues with recent bcftools, which are more picky about
  input files:
  - Avoid bcftools concat errors with all empty inputs.
  - Remove problematic FreeBayes annotations which no longer match
    header requirements after decomposition.
- Fix logging to correctly raise errors on failures.

v0.2.1

v0.2.1: square fix for redundant DP filters to bcftools

Recent versions of bcftools will not process ambiguous filter
specifications like `DP` when present in both INFO and FORMAT files.
This clarifies intent to avoid errors. Thanks to @ohofmann

v0.1.9

v0.1.9: Remove usage of gatk-framework; replace with bcftools

Removes usage of older GATK3 gatk-framework, replacing with
modern bcftools equivalents. gatk-framework is no longer distributed
with bcbio. bcbio/bcbio-nextgen#2412

v0.1.8

v0.1.8: fix tabix index error for variants at position 1 of contigs.

Fixes chapmanb/bcbio-nextgen#2383

v0.1.7

v0.1.7: Avoid FreeBayes error when running variant-input without an e…

v0.1.6

Handle non-bgzipped ensemble outputs

Convert these inputs to bgzipped output to avoid GATK issues writing
the index. Fixes #10