Revert "bump sqlite"

This reverts commit 9f128db.

.github/workflows/build.yml

@@ -3,7 +3,7 @@ on: [push, pull_request]
 
 env:
   APT_DEPS: libzstd-dev samtools tabix libhts-dev pigz python3-pip libcurl4-openssl-dev
-  BREW_DEPS: [email protected] zstd samtools pigz coreutils sqlite
+  BREW_DEPS: [email protected] zstd samtools pigz coreutils
   PIP_DEPS: pytest pytest-xdist
 
 jobs:
@@ -126,6 +126,12 @@ jobs:
         for dep in $BREW_DEPS ; do
           brew install $dep || brew upgrade $dep
         done
+
+        # FIXME 2022-12-27: pin sqlite 3.39.4 due to query plan regression in 3.40.0
+        #                   https://sqlite.org/forum/forumpost/07b36e3899a9ae21
+        wget https://raw.githubusercontent.com/Homebrew/homebrew-core/fc08979e0cc7c580a2feba5447d9a518dc518826/Formula/sqlite.rb
+        brew reinstall -s sqlite.rb
+
         /usr/local/bin/pip3 install $PIP_DEPS
     - name: rust toolchain
       uses: actions-rs/toolchain@v1

Dockerfile

@@ -4,7 +4,7 @@
 FROM centos:7 as builder
 
 ARG CMAKE_VERSION=3.17.3
-ARG SQLITE_VERSION=3400100
+ARG SQLITE_VERSION=3390400
 ARG ZSTD_VERSION=1.5.2
 ARG CPU_ARCH=ivybridge
 ENV CFLAGS="-march=${CPU_ARCH} -O3"