perf: build htslib with libdeflate for faster BGZF/BAM decoding

WORKSPACE

@@ -29,6 +29,19 @@ http_archive(
     ],
 )
 
+# libdeflate is a faster DEFLATE/gzip codec than zlib. htslib uses it for bgzf
+# (BAM) (de)compression when built with HAVE_LIBDEFLATE; BAM bgzf decoding is the
+# dominant codec cost when reading reads in make_examples.
+http_archive(
+    name = "libdeflate",
+    build_file = "//:third_party/libdeflate.BUILD",
+    sha256 = "ed1454166ced78913ff3809870a4005b7170a6fd30767dc478a09b96847b9c2a",
+    strip_prefix = "libdeflate-1.20",
+    urls = [
+        "https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.20.tar.gz",
+    ],
+)
+
 http_archive(
     name = "libssw",
     build_file = "//:third_party/libssw.BUILD",

third_party/htslib.BUILD

@@ -217,6 +217,7 @@ genrule(
         echo '#define HAVE_GMTIME_R 1'
         echo '#define HAVE_INTTYPES_H 1'
         echo '#define HAVE_LIBBZ2 1'
+        echo '#define HAVE_LIBDEFLATE 1'
         echo '#define HAVE_LIBLZMA 1'
         echo '#define HAVE_LIBZ 1'
         echo '#define HAVE_MEMORY_H 1'
@@ -273,7 +274,10 @@ cc_library(
     linkopts = extra_libs,
     textual_hdrs = textual_hdrs,
     visibility = ["//visibility:public"],
-    deps = [":htslib_deps"],
+    deps = [
+        ":htslib_deps",
+        "@libdeflate",
+    ],
 )
 
 # Misc binaries that might be exported.

third_party/libdeflate.BUILD

@@ -0,0 +1,23 @@
+# Description:
+#   libdeflate - fast DEFLATE/zlib/gzip compression and decompression.
+#   Used by htslib (when HAVE_LIBDEFLATE is set) to accelerate bgzf (BAM)
+#   (de)compression.
+
+licenses(["notice"])  # MIT
+
+exports_files(["COPYING"])
+
+# All architecture-specific sources are guarded by ARCH_* #ifdefs and compile to
+# nothing on non-matching targets, so it is safe to compile every lib/**/*.c.
+cc_library(
+    name = "libdeflate",
+    srcs = glob([
+        "lib/**/*.c",
+        "lib/**/*.h",
+        "common_defs.h",
+    ]),
+    hdrs = ["libdeflate.h"],
+    copts = ["-O3"],
+    includes = ["."],
+    visibility = ["//visibility:public"],
+)