v0.9.4

• Fix a concurrency bug introduced by fixing the prior concurrency bug in v0.9.3
• Update SQLite & Zstandard versions

---

Start here 👉 👈

Most developers should install a package through pip/conda/maven/cargo. They bundle the same prebuilt library files available below; the latter can be used with C/C++ projects and yet-to-be-packaged languages.

• libgenomicsqlite.so for Linux x86-64 (Ivy Bridge), built in CentOS 7
• libgenomicsqlite.dylib for macOS Catalina x86-64

An up-to-date version of SQLite itself (≥3.31.0) is also required, as detailed in the docs. If unable to upgrade the host SQLite, a prebuilt Linux x86-64 libsqlite3.so.0 is available below, for deployment with suitable LD_LIBRARY_PATH.

USE AT YOUR OWN RISK: This project is not associated with the SQLite developers.

---

_{SHA-256 digests:}

baa1440514341f2f5327b66fa8d94d4752b7bfab4a27e266c3cd9d6377310f79  libgenomicsqlite.so
4be1a68c6894664bb88c56aedd1b63c31d846c9d6d1eb7e1dd69c40510494b88  libgenomicsqlite.dylib
4485b89bfcac56ae20dd0ecfbca07f6a6cd53f59f18eb3a31ce6cc4d2f322950  genomicsqlite-jdbc-v0.9.4.jar
56d8684bd694cecbd1961cb690c360c8d02e03665a2e7d7ec780ddda47821367  libsqlite3.so.0

v0.9.3

• Fix a concurrency bug potentially causing corruption in a multithreaded process writing multiple database files simultaneously.
• Notice: the newest SQLite versions as of this writing, v3.40.0 and v3.40.1, have a query planning regression moderately impacting GRI query performance. A fix is expected in SQLite's next minor version. In the meantime, affected projects should pin SQLite v3.39.4 if possible.

---

_{SHA-256 digests:}

b57cecf021473959733c5c8b699967d320baca62f80b87e2575cb6014695c768  libgenomicsqlite.so
5a900bbecf5e7add3d6c60d3a5fec000f072de5a5e9328ddd79c107168b357e0  libgenomicsqlite.dylib
bbe1501f12a691ae813397dc190defd9a40f4a6c3fa7baa76ff3d5adc6eb6deb  genomicsqlite-jdbc-v0.9.3.jar
09b5f5b30785413789375cd51c76bdb6131ea3ac5982e4c5959c84329f3cab9b  libsqlite3.so.0

v0.9.2

• Set pragma secure_delete = ON automatically, to ensure that deleting data shrinks the compressed file commensurately
• Bump zstd_vfs and SQLite versions

---

_{SHA-256 digests:}

6386d4e319e3e6b744295e12343ca0e8f0a33439a7955e490b5994e84335ad1a  libgenomicsqlite.so
0778ac735a850f68c58c071602394fabfb805d7f6d3476e6eae49bf45eec31cf  libgenomicsqlite.dylib
f9fdec286995fd82cf9383739cf2a7d02287e586bc4de4547172772a06f2df34  genomicsqlite-jdbc-v0.9.2.jar
d992d938246ca4b8ee3f242578defcb5d80c40f097e9e4f418d7c33fcd73ffc6  libsqlite3.so.0

v0.9.1

• Simplified usage of genomic_range_index_levels()
  
  The genomic_range_index_levels() helper for the GRI level bounds optimization now caches its analysis across subsequent invocations on the same SQLite connection (so long as the database isn't modified in the meantime). This means the in-SQL helper can be inlined into queries, instead of the driver program invoking it separately beforehand, in most cases. (If querying one item at a time, the latter approach would still be slightly more efficient.)

• Streamlined web access with .dbi helper files (experimental)
  
  Access to compressed databases over HTTP[S] can now be made more efficient with a small .dbi helper file served alongside. The genomicsqlite command-line utility can generate the .dbi helper for a given read-only database, while the client automatically probes for it by appending .dbi to the main URL.
  
  The .dbi is a compilation of key index pages from the main database file. Using this is optional, but often helpful for big databases accessed with high-latency requests. Without, the client might need to issue many small requests to collect those pages.

• Bumped zstd, SQLite, rust dependencies

---

_{SHA-256 digests:}

e0b15a0e5a7c5f65f754fe5cf7cfcb581a122d70f741d9d27af13c9d6dbf60cc  libgenomicsqlite.so
f910fc659bbd5fa393bd251f807348eb1a7b4e96535fc509efc9e7267e4fed65  libgenomicsqlite.dylib
4a226c92c5fa565230e2ad693895464b4e1b2cf8b60a1e7d94c678b8028038c0  genomicsqlite-jdbc-v0.9.1.jar
8b4c0c422f9ad8a61b5ff42603bd340259b6029450e90265e7a5cfc5d66ede87  libsqlite3.so.0

v0.9.0

Withdrawn

v0.8.1

Improves efficiency of prefetching logic for web access to database files

---

_{SHA-256 digests:}

b7403da1741c01f068ff2f38ecce908a2b4a9034dbfce726e2114e1f234e5f64  libgenomicsqlite.dylib
66ca6e20936fbffadb4397743b96db57bd21af59a618d8ca9be033916a1f3a5f  libgenomicsqlite.so
82634336f07b948d74b539a741f3fd9a9a3222c41955c86711ebb596b0621716  genomicsqlite-jdbc-v0.8.1.jar
2dae78da03f2dd1bdeac5089cf4ec976912efab23186e5b6c0c8ce91048d16b9  libsqlite3.so.0

v0.8.0

• Compressed database files can be queried over the web directly (docs)
  • Open routines accept http/https URLs (read-only) as well as local filenames
  • Adaptive batching & prefetching to optimize the HTTP request pattern (will be tuned over time)
  • Builds in sqlite_web_vfs extension (also usable standalone)
• Improves the genomicsqlite command-line tool installed with the Python package (docs)
  • Opens local filename or remote URL
  • Removes extraneous messages on entering interactive shell
  • New --compact subcommand to re-compress and defragment a database file, potentially shrinking it further and making it more suitable for web access
• The extension is now compatible with host programs statically linking SQLite3.

---

Start here 👉 👈

Most developers should install a package through pip/conda/maven/cargo, which bundle the same prebuilt library files available below for use with C/C++ and yet-to-be-packaged languages.

• libgenomicsqlite.so for Linux x86-64 (Ivy Bridge), built in CentOS 7
• libgenomicsqlite.dylib for macOS Catalina x86-64

An up-to-date version of SQLite itself (≥3.31.0) is also required, as detailed in the docs. If unable to upgrade the host SQLite, a prebuilt Linux x86-64 libsqlite3.so.0 is available below, for deployment with suitable LD_LIBRARY_PATH.

USE AT YOUR OWN RISK: This project is not associated with the SQLite developers.

---

_{SHA-256 digests:}

610d5de2f12906b098528c391a1af9a9bdb09561f1b6e795a2c739d533fcf5c6  libgenomicsqlite.so
80e22ff126561d379210363c842f95101a1cdd9a94d687a342cabadf0e0add24  libgenomicsqlite.dylib
9d6cd9c6724d276db4d3b1a344d72cd96bfa2bda99e4702033647b6bf481f8b6  genomicsqlite-jdbc-v0.8.0.jar
2dae78da03f2dd1bdeac5089cf4ec976912efab23186e5b6c0c8ce91048d16b9  libsqlite3.so.0

v0.8.0-pre.0

docs & testing for v0.8.0 (#15)

v0.7.0

Linux x86-64 build improvements:

• Extends prebuilt shared library (.so) compatibility back to CentOS 7 and Ivy Bridge CPUs
• Each Release will now include a prebuilt libsqlite3.so.0, as a backup option for those unable to upgrade their host's SQLite

USE AT YOUR OWN RISK: The extension makes fundamental changes to the SQLite storage layer. While designed to preserve ACID transaction safety, it's young and unlikely to have zero bugs. This project is not associated with the SQLite developers.

---

_{SHA-256 digests:}

6d03fc963752b82ae7cfbffb56aef21d9ccbeaf3c5728d3f3d499c58d53d1917  libgenomicsqlite.so
732e4f39842206d49e6cc01c8d620957aa810ba63fd12ce3c010fc5bbf02aa92  libgenomicsqlite.dylib
507b2542fb8dd8b2c9359102dbf0b304061effae481b4b914f9d60a16200b29e  genomicsqlite-jdbc-v0.7.0.jar
3873c8aa004a88e27b9029d5d9442b9ae52875cacf9aa339b773154844d27bf2  libsqlite3.so.0

v0.6.0

• Add in-SQL dna_revcomp(?) to reverse-complement a DNA sequence TEXT value
• The SQLite developers' UINT collating sequence is now bundled and enabled automatically
  • useful for sorting by chromosome names (e.g. 'chr2' < 'chr10') and other identifiers
  • simply ORDER BY chrom COLLATE UINT
• Use speedier Zstandard v1.4.7 internally
• Portability tweaks to prebuilt shared library