Paragraph v2.4a

Update from our revised manuscript!

• Update manuscript link and paper data
• BP_DEPTH and BP_NO_GT moved from FT to VCF filter field for better precision
• Interface fix for options, warning message and python tests

Paragraph v2.3

• Add more informative warnings for malformatted VCF
• Idxdepth now ignores ALT contig by default
• Update README for run time and population-scale genotyping

Paragraph v2.2b

• Add static build in release (require gcc 5.2+, linux system)
• Documentation update

Paragraph-v2.2a

• Update license to Apache 2.0
• Fix docker entry point and version

Paragraph v2.2

• Rewrote README. Include our preprint and data
• VCF now output genotypes for all samples in manifest
• Internal htslib updated (v1.8 -> 1.9)
• Fix on padding base issues in <DEL>
• Now support <DUP> and <INV>
• Better error handling in VCF-JSON conversion
• Support for python 3.4 & 3.5
• Temporarily removed the included Boost support from PR #9 and #10

v2.1 release

Include fixes and optimizations on:

• Recognition of chrX and Y.
• Better filters for genotypers
• Better depth test method (poisson->normal)