0.7.0 Beta 3

Changes:

• a7f86da Merge pull request #225 from TileDB-Inc/ss/tiledb-2.1.4
• ec05524 Update to TileDB 2.1.4
• 3bec8c9 Merge pull request #216 from TileDB-Inc/sethshelnutt/ch4458/ingestion-in-fragments-split-by-contig
• 4f05c04 V4 writes should split fragments by contig
• ce113d2 Merge pull request #215 from TileDB-Inc/sethshelnutt/ch4459/remove-sample-batching-from-reads
• 48e1e0a Merge pull request #217 from TileDB-Inc/ss/add-ingestion-query-buffer-option
• 1d6d160 Merge pull request #213 from TileDB-Inc/ss/option-disable-vcf-header-stats
• c28816d Add CLI option for max TileDB buffer size
• 4378baa Merge pull request #219 from TileDB-Inc/ss/add-verbose-message-ingestion
• 2a40ed2 Merge pull request #221 from TileDB-Inc/ss/handle-special-case-all-sample-export

See More

• f1df5f3 Handle all sample export for v4 with optimal range
• 8de6315 Reset pandas index for python unordered tests
• a674f7e Merge pull request #223 from TileDB-Inc/ss/python-test-handle-unordered-results
• 60a775b Merge pull request #218 from TileDB-Inc/ss/store-contig-vcf-ingestion
• 06fd841 Sort pandas df's for unordered comparison
• a93c63c Merge pull request #222 from TileDB-Inc/revert-203-ss/workaround-osx-ci-homebrew-openssl
• 2ed3f3b Revert "Workaround homebrew openssl error for CI"
• 05570a6 Fix writer init with parameters
• 00aee70 Add option for enable/disable of vcf header stats
• 528f0e3 Merge pull request #210 from TileDB-Inc/ss/optimize-v4-processing-with-single-contig-query
• 8a4ae80 Add write message for verbose ingestion
• b6e9585 Set the contig for ingestion on seek of VCF file
• 0b63c64 Don't batch v4 reads by samples
• c5ae2ea Remove contig check from process_query_results_v4
• 93ed1d3 Merge pull request #209 from TileDB-Inc/ss/support-tiledb-2.2-est-result-api-change
• c384d5d Support TileDB 2.2 C++ result estimate API changes
• e3d50b6 Merge pull request #212 from TileDB-Inc/revert-198-vn/build-chunked-arrow-table
• 0e163ab Revert "Build Chunked Arrow Table in _read_partition()"
• f75d34b Merge pull request #198 from TileDB-Inc/vn/build-chunked-arrow-table
• d75b35d Merge pull request #208 from TileDB-Inc/sethshelnutt/ch4407/3d-array-ingestion-need-to-write-in-lexigraphical
• 63ad03b Sort regions in lexicographical order for v4 writes
• 975dad3 Merge pull request #207 from TileDB-Inc/ss/only-fetch-header-on-sample-batch-change
• b199c0f Only fetch vcf headers on a new read sample batch
• 9c077d5 Merge pull request #206 from TileDB-Inc/ss/split-read-path-v4
• 6983823 Split init_for_reads/next_read_batch into versions
• c16499a Merge pull request #204 from TileDB-Inc/ss/reduce-array-opens
• 71314c5 Merge pull request #202 from TileDB-Inc/ss/add-python-format-linting
• 5117f69 Merge pull request #197 from TileDB-Inc/ss/hfile-destroy
• bfa68ce Merge pull request #205 from TileDB-Inc/ss/v2-v3-query-optimizations
• 31dd235 Optimize v2/v3 read queries
• c448dd8 Merge pull request #201 from TileDB-Inc/ss/prebuilt-tiledb
• 3e80dd4 Merge branch 'master' into vn/build-chunked-arrow-table
• 323b04e Fix leaking of hfile* on file open errors
• e16baf2 Modify read() and continue_read() To Take return_type Arg
• f9ddd66 Add build matrix to test building tiledb from source
• da55340 Use prebuilt artifacts by default for TileDB
• 90695d6 Format additional python scripts
• bc2daea Add python format and linting check
• 075188c General cleanup of unneeded parameters in Dataset
• 17e264f Share open data array w/reader and dataset classes
• 14f4eef Don't reopen the array on every read query
• defe57e Add data/vcf array pointers to Dataset class
• b74a06e Merge pull request #203 from TileDB-Inc/ss/workaround-osx-ci-homebrew-openssl
• f8c2107 Workaround homebrew openssl error for CI
• 99e85c6 Build Chunked Arrow Table in _read_partition()
• 2afe1dd Merge pull request #199 from TileDB-Inc/ss/format-python
• b1422d0 Format with black
• dc64ce9 ASAN fixes
• 09bb52c Adjust writer init to allow setting config
• c549054 Fix region sorting for reads
• ef3631d Fix edge case in region overflow
• dc4cf3f Only register samples for v2/v3 datasets in python
• 4747b4d Switch writer to own a dataset unique_ptr
• e071db3 Remove registration for v4 arrays
• 2ea9a69 New v4 test arrays
• b390173 Merge pull request #194 from TileDB-Inc/ss/string-sample-id-query-by-contig
• b3b4f84 Swich v4 record writting to avoid shared_ptr copy
• febceb5 General cleanup
• 9b75294 Cleanup
• 20c2311 Update V4 unit test arrays
• 783a9ea Switch dimension ordering to contig,start_pos,sample
• f81abc3 Switch order of contig and start_pos dimensions
• e1c7df3 Query ranges by contig
• 6a732b8 Fix coalescing ranges in v4
• f0bbbc1 Optimize contig map lookup for processing
• 7888678 Update python test ordering
• fdfd77f Fix ordering in cli tests
• e86c0f9 Workaround est results returning 0 for offests
• 5895cd9 Update unit-vcf-export tests based on new ordering of partitions
• 1f47a55 Fix report_cell from rebase
• 021a37e Test updates for more order issues, pt.3
• 0c78652 Test updates for more order issues, pt:2
• 01e0214 Test updates for more order issues
• 083c0cc Improve run-cli test with context output
• 5067a8e Switch sample to a string dimension
• 3239a74 Set java/spark version for 0.7.0-SNAPSHOT
• 7b50da8 Cleanup
• 53eda54 Binary search over contig regions and exit early
• 282ef97 Fix warning for different sign comparison
• 3028d95 Don't use contig index hash, might be too expensive
• 44df482 Switch to using point ranges for all sample ids
• 6fb7cf9 Switch to do not report logic for intersection
• c3c5951 Add new v4 dataset schema with 3D array.
• d1189e7 Merge pull request #181 from TileDB-Inc/ss/asan
• 66110c9 Switch htslib plugin to not use unique_ptrs for ctx/cfg
• 28dbb0e Fix context leak in htslib plugin setup
• 81c2b21 Add support for ASAN

This list of changes was auto generated.