v1.3.2

--with-missing-fields: fill missing ref AD with DP,0

v1.3.1

--with-missing-fields: pad AD & PL to the expected vector length (with missing values) for biallelic sites

v1.3.0

• Add spvcf decode --with-missing-fields flag to fill in all trailing FORMAT fields, even when their values are missing.
• Update htslib & libdeflate versions

v1.2.0

• Fix omission of QC field(s) when DP isn't present (#26 @RussellTaylor)
• Update htslib and libdeflate versions
• Executable target architecture advanced to Haswell (from Ivy Bridge)
• Published Docker image
• Modernize spvcf.wdl

v1.1.0

• Update the linked htslib version
• Modernize WDL wrappers
• Minor speed improvements

v1.0.0 🍾

User can increase (or decrease) the resolution of DP rounding during QC squeezing, using -r/--resolution

20201226

Fail-fast if libdeflate isn't available

release candidate

• spvcf encode: perform QC squeezing by default (opt-out)
• rewrite header e.g. ##fileformat=VCF4.2 to ##fileformat=spVCFvx.y.z-gabcdef;VCF4.2 and back
• error message if input stream needs decompression
• warning message if input stream doesn't start with expected ##fileformat
• htslib 1.9

Don't quote-encode cells whose genotypes aren't reference-identical or non-called

This spec change ensures that all non-reference genotypes on a spVCF row can be read without referring to any previous row, a significant convenience in exchange for a negligible size increase (as the affected case, a run of non-reference genotypes with exactly repeated QC values down a column, is extremely rare).

v0.5.0: Multithreaded encoder (#13)

The encoder can run multithreaded by buffering batches of input lines and processing each batch in a worker thread. In favorable circumstances this yields higher throughput than the default single-threaded approach, but there is a trade-off of greatly increased memory usage and copying. Activated with -t,--threads.