Fix meson/ninja build

README.md

@@ -219,15 +219,31 @@ meson build
 cd build
 ninja
 ninja test
+
+time ./build/sambamba sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
+sambamba 1.0.1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2023
+    LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)
+real    0m13.343s
+user    2m11.663s
+sys     0m4.232s
 ```
 
-or possibly with some additional tuning
+or possibly with some additional tuning runtimes get close to the optimized static build (see [benchmarks](test/benchmark/stats.org).
 
 ```sh
 rm -rf build/ ; env D_LD=gold CC=gcc meson build --buildtype release
 cd build/
 env CC=gcc ninja
 env CC=gcc ninja test
+
+time ./build/sambamba sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
+sambamba 1.0.1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2023
+    LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)
+real    0m10.227s
+user    2m7.203s
+sys     0m4.039s
 ```
 
 ## Compiling for MacOS

guix.scm

@@ -2,13 +2,6 @@
 ;;
 ;;   guix shell -C -D -f guix.scm -- bash --init-file <(echo "ln -s /bin/sh /bin/bash")
 ;;
-;; and build
-;;
-;;   find -name CMakeCache.txt|xargs rm -v
-;;   cd build
-;;   cmake -DCMAKE_BUILD_TYPE=Debug ..
-;;   cmake --build . --verbose -- -j 14 && ctest . --verbose
-;;
 ;; For the tests you may need /usr/bin/env. In a container create it with
 ;;
 ;;   mkdir -p /usr/bin ; ln -s $GUIX_ENVIRONMENT/bin/env /usr/bin/env
@@ -27,12 +20,15 @@
   (guix gexp)
   (gnu packages base)
   (gnu packages bioinformatics) ; for samtools in sambamba
+  (gnu packages build-tools) ; for meson
   (gnu packages compression)
   (gnu packages curl)
   (gnu packages dlang)
   (gnu packages gcc)
+  (gnu packages pkg-config)
   (gnu packages perl)
   (gnu packages python)
+  (gnu packages ninja)
   (gnu packages ruby)
   (gnu packages tls)
   (gnu packages version-control)
@@ -77,6 +73,9 @@
       (inputs
        `(("samtools" ,samtools) ; for pileup
          ("bcftools" ,bcftools) ; for pileup
+         ("meson" ,meson) ; for testing meson build system
+         ("ninja" ,ninja)
+         ("pkg-config" ,pkg-config)
          ("lz4" ,lz4)
          ("lz4-static" ,lz4 "static")
          ("zlib-static" ,zlib "static")

meson.build

@@ -8,7 +8,7 @@
 
 project('Sambamba', ['c','d'],
     license : 'GPL-2.0',
-    version : '1.0.0',
+    version : '1.0.1',
     # default_options : ['buildtype=debugoptimized']
 )
 
@@ -29,7 +29,7 @@ endif
 
 # The optimized flags are
 # ldc2 -singleobj -wi -I. -IBioD -g -J. -O3 -release -enable-inlining -boundscheck=off -L-lz -c -of=bin/sambamba-0.8.2.o
-extra_dflags = [ '-I../BioD','-g','-release','-boundscheck=off']
+extra_dflags = [ '-I../BioD','-I../BioD/contrib/msgpack-d/src','-g','-release','-boundscheck=off','-enable-inlining','-singleobj']
 extra_ldflags = ['-L=-flto=full']
 
 #
@@ -176,8 +176,18 @@ cram_src = [
 ]
 
 thirdparty_src = [
-    'thirdparty/mergesort.d',
-    'thirdparty/unstablesort.d'
+'thirdparty/mergesort.d',
+'thirdparty/unstablesort.d',
+'BioD/contrib/msgpack-d/src/msgpack/attribute.d',
+'BioD/contrib/msgpack-d/src/msgpack/common.d',
+'BioD/contrib/msgpack-d/src/msgpack/package.d',
+'BioD/contrib/msgpack-d/src/msgpack/register.d',
+'BioD/contrib/msgpack-d/src/msgpack/unpacker.d',
+'BioD/contrib/msgpack-d/src/msgpack/buffer.d',
+'BioD/contrib/msgpack-d/src/msgpack/exception.d',
+'BioD/contrib/msgpack-d/src/msgpack/packer.d',
+'BioD/contrib/msgpack-d/src/msgpack/streaming_unpacker.d',
+'BioD/contrib/msgpack-d/src/msgpack/value.d',
 ]
 
 manpages = [

test/benchmark/stats.org

@@ -55,6 +55,13 @@ sys     0m0.240s
 
  time ./bin/sambamba-1.0.0 sort HG00100.chrom20.ILLUMINA.bwa.GBR.low_coverage.20130415.bam
 
+sambamba 1.0.1
+ by Artem Tarasov and Pjotr Prins (C) 2012-2023
+    LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)
+real    0m9.599s
+user    2m1.039s
+sys     0m3.834s
+
 sambamba 1.0.0
  by Artem Tarasov and Pjotr Prins (C) 2012-2022
     LDC 1.32.0 / DMD v2.102.2 / LLVM14.0.6 / bootstrap LDC - the LLVM D compiler (1.32.0)