From cdb73f51a06e618a5d7d73d9e9a178c13bdb928e Mon Sep 17 00:00:00 2001
From: Pjotr Prins <pjotr.public01@thebird.nl>
Date: Sat, 31 Jul 2021 11:29:40 +0200
Subject: [PATCH] Fix build for LDC 1.26.0 and LLVM 9.0.1 - tests pass

---
 .guix-build        | 3 ++-
 INSTALL.md         | 7 +++++--
 Makefile.guix      | 4 ++--
 RELEASE-NOTES.md   | 1 +
 VERSION            | 2 +-
 sambamba/pileup.d  | 1 +
 test/test_suite.sh | 4 ++--
 7 files changed, 14 insertions(+), 8 deletions(-)

diff --git a/.guix-build b/.guix-build
index 2459bd29..56a88cd9 100644
--- a/.guix-build
+++ b/.guix-build
@@ -1,3 +1,4 @@
 # This command creates a build container for Sambamba using GNU Guix
 
-guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib
+env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics \
+guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim zlib $*
diff --git a/INSTALL.md b/INSTALL.md
index 84834ce5..39455452 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -18,7 +18,7 @@ and run our development setup (gold was added lately by ldc)
 
     guix environment -C guix --ad-hoc gcc-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
     make clean
-    make -f Makefile.guix -j 4
+    env CC=gcc make -f Makefile.guix -j 4
     make -f Makefile.guix check
 
 this way all dependencies are isolated. To create a static release use
@@ -31,7 +31,10 @@ We use GNU Guix containers for development. Install Guix and run a build
 container with
 
     . .guix-build
-    make -f Makefile.guix
+    make -f Makefile.guix clean
+    # build the debug version
+    env CC=gcc make -f Makefile.guix lz4-static -j 8
+    env CC=gcc make -f Makefile.guix -j 8
     make -f Makefile.guix check
 
 Note that this also works in the emacs shell.
diff --git a/Makefile.guix b/Makefile.guix
index cd37ce72..adc08342 100644
--- a/Makefile.guix
+++ b/Makefile.guix
@@ -31,7 +31,7 @@ LIBS   = -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a
 
 LIBS_STATIC = $(DLIBS) lz4/lib/liblz4.a
 SRC         = $(wildcard main.d utils/*.d thirdparty/*.d) $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d BioD/bio/*/*/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
-OBJ    = $(SRC:.d=.o) utils/ldc_version_info_.o
+OBJ    = $(SRC:.d=.o)
 OUT    = bin/sambamba-$(shell cat VERSION)
 static: OUT += -static
 
@@ -116,7 +116,7 @@ clean-c:
 	rm -v lz4/lib/*.[oa]
 
 clean-d:
-	rm -v $(OBJ) $(OUT) trace.{def,log}
+	rm -v $(OBJ) $(OUT) # trace.{def,log}
 	rm -v bin/*
 
 clean-tests:
diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md
index db93b4c1..14094905 100644
--- a/RELEASE-NOTES.md
+++ b/RELEASE-NOTES.md
@@ -2,6 +2,7 @@
 
 + Some FASTA unittests break when they write to disk and read after -
   marked with ~version(Broken)~
++ Fix build for LDC 1.26.0 and LLVM 9.0.1
 
 ## ChangeLog v0.8.0 (20201130)
 
diff --git a/VERSION b/VERSION
index a3df0a69..4cac817b 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.8.0
+0.8.1-pre1
diff --git a/sambamba/pileup.d b/sambamba/pileup.d
index 3a746784..010afca2 100644
--- a/sambamba/pileup.d
+++ b/sambamba/pileup.d
@@ -749,4 +749,5 @@ int pileup_main(string[] args) {
           return 1;
         }
     }
+    return 0;
 }
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 960b3f42..7e4c35e6 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -5,7 +5,7 @@ sambamba=$1
 if [ ! -f $sambamba ]; then
     sambamba=./bin/sambamba
 fi
-opts="-q"
+opts="-q --DRT-testmode=run-main"
 outdir=output
 mkdir -p $outdir
 
@@ -207,7 +207,7 @@ testIssue356(){
     assertEquals 0 $?
 }
 
-testIssue421(){ 
+testIssue421(){
     # sambamba-markdup: not enough data in stream https://github.com/biod/sambamba/issues/421
     cat test/issue_204.bam | $sambamba $opts markdup /dev/stdin test.bam 2> /dev/null
     # assertEquals 0 $?  Disable test until we have a single pass, see issue 421