Releasing 0.6.9

Author: pjotrp

BioD

@@ -18,9 +18,9 @@ possibleto install the build tools with GNU Guix
     guix package -i gcc gdb bash ld-wrapper ldc which python2 git
 
 Even better, with Guix, you can create a light-weight container in the source tree
-and run our development setup
+and run our development setup (gold was added lately by ldc)
 
-    guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
+    guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git binutils-gold
     make clean
     make -j 4
     make check

INSTALL.md

@@ -34,7 +34,7 @@ DLIBS       = $(LIBRARY_PATH)/libphobos2-ldc.a $(LIBRARY_PATH)/libdruntime-ldc.a
 DLIBS_DEBUG = $(LIBRARY_PATH)/libphobos2-ldc-debug.a $(LIBRARY_PATH)/libdruntime-ldc-debug.a
 LIBS        = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lpthread -L-lm
 LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a
-SRC         = utils/ldc_version_info_.d utils/lz4.d utils/strip_bcf_header.d $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d) utils/version_.d $(sort $(wildcard thirdparty/*.d cram/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d))
+SRC         = utils/ldc_version_info_.d utils/lz4.d utils/strip_bcf_header.d $(sort $(wildcard BioD/contrib/undead/*.d BioD/contrib/undead/*/*.d)) utils/version_.d $(sort $(wildcard thirdparty/*.d cram/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio/*/*/*/*.d BioD/bio/*/*/*/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d))
 OBJ         = $(SRC:.d=.o)
 OUT         = bin/sambamba
 

Makefile

@@ -1,4 +1,4 @@
-## ChangeLog v0.6.9-pre
+## ChangeLog v0.6.9 (20190313)
 
 + Added support for Picard style sorting, see https://github.com/biod/sambamba/issues/369 - thanks https://github.com/TimurIs
 + Add a new sorting option to pull together mates when sorting by read name, see https://github.com/biod/sambamba/pull/380 - thanks https://github.com/emi80

RELEASE-NOTES.md

@@ -1,7 +1,7 @@
 /*
     This file is part of Sambamba.
     Copyright (C) 2012-2017    Artem Tarasov <lomereiter@gmail.com>
-    Copyright (C) 2012-2018    Pjotr Prins <pjotr.prins@thebird.nl>
+    Copyright (C) 2012-2019    Pjotr Prins <pjotr.prins@thebird.nl>
 
     Sambamba is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -87,7 +87,7 @@ For bug reports and feature requests see
 
 void printVersion() {
     stderr.writeln();
-    stderr.writeln("sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2018");
+    stderr.writeln("sambamba " ~ VERSION ~ " by Artem Tarasov and Pjotr Prins (C) 2012-2019");
     stderr.writeln("    LDC " ~ LDC_VERSION_STRING ~ " / DMD " ~ DMD_VERSION_STRING ~
      " / LLVM" ~ LLVM_VERSION_STRING ~ " / bootstrap " ~ BOOTSTRAP_VERSION_STRING);
     stderr.writeln();

sambamba/main.d

@@ -1,6 +1,6 @@
 module utils.version_;
 
-immutable string VERSION = "0.6.8";
+immutable string VERSION = "0.6.9";
 immutable string HEADER_VERSION = "1.0"; // goes in header for reproducibility between sambamba versions
 
 import bio.std.hts.sam.header;