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@jonathonl jonathonl released this 31 Aug 20:58
· 6 commits to master since this release
v2.1.0
99d85c2
  • Fixes issues in docker packaging.
  • Adds missing #include for to files that are using std::numeric_limits
  • Fixes error message when piping export output.
  • Allows modifying BGZF compression level and sets the default level to 6 for both BGZF and ZSTD.
  • Fix for environments where char is unsigned.
  • Fix for setting max block size of 65536.
  • Updates shrinkwrap to fix broken zlib URL.
  • Fixes bug in automatic updates to standard INFO fields.
  • Validates data types when writing BCF.
  • Crossplatform fix for sprintf with 64-bit integers.
  • Improves speed of writing VCF individual data.
  • Fixes for type thinning.
  • Removes FORMAT column from header line with no individual data.
  • Fixes index file check during import/export.
  • Allows reading of VCF files that are missing INFO or FORMAT headers (assumes String type).
  • Terminates immediately after write failure is encountered during import/export.
  • Fixes bug where last record of VCF file was dropped.
  • Fixes "Number" in SAV file GT header.
  • Removes IDX header field when writing new files.
  • Bug fix for header IDX being out of order.
  • Fixes bug in copy_as_dense().
  • Index query changes to support temporary files.
  • Fixes serialization bugs related to missing and end_of_vector values.
  • Fixes for is_missing() and is_end_of_vector().
  • Fixes is_end_of_vector() for floating point types.
  • Adds support for "end of vector" with stride_reduce().
  • Fixes region compare bug.
  • Adds support for INFO/END when performing index queries.
  • Fixes BCF rlen and adds support for indexing INFO/END.
  • Inherit site_info assignment operator to variant class.
  • Fixes deserialize_vec when size and type are zero.
  • Fixes parsing of VCF Flag INFO fields.
  • Removes "no-tree-vectorize" attributes now that data vectors are aligned.
  • Replaces flat buffer design for typed_value so that data vectors are memory aligned.
  • Adds get-dependencies.cmake as alternative to cget.
  • Fixes issues with Github workflow.
  • Fixes big endian bugs.
  • Updates endianess swapping behavior to reflect latest BCF spec.
  • Fixes bug in PBWT unsort.
  • Gracefully skips PBWT for vectors with bit widths greater than 16.
  • Bug fixes for multi-format files.
  • Updates shrinkwrap version to fix open_mode bug.
  • Adds conda instructions to readme.
  • Updates shrinkwrap to fix link error when liblzma is not available.
  • Fix for sample subsetting of SAV v1 files.
  • Add experimental sparse regression tool.
  • Fixes examples in README.
  • Fixes eval link error.
  • Adds find_dependency to export config for proper import of shrinkwrap into downstream projects.
  • Moves SAVVY_VERSION defintion from CLI to library target.
  • Adds support for individual data of type String.
  • Links shrinkwrap package instead of directly linking zlib and zstd libs.
  • Reorders fields in auto-generated FORMAT headers to be consistent with VCFs in htsspec examples.
  • Removes extra line from end of stat-merge output.
  • Adds --filter option to stat sub-command and removes n_singletons column from per-sample output.
  • Adds per-AC stats.
  • Adds stat-merge sub-command and per-sample statistics to stat sub-command.
  • Adds support for tabix (.tbi) index files.
  • Fixes regression in CSI interval merging.
  • Fixes bad flag being set when EOF is reached with sites-only VCFs.
  • Updates CSI index parsing to support unbounded ends and mimic htslib behavior.
  • Removes --data-format option from export sub-command.
  • Fixes VCF parsing of sites-only files.
  • Fixes exit status for head sub-command.
  • Adds sparse_vector class (compressed_vector alternative).
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