From 495567f509d942e01bc77d99d88729c96755a405 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 13 Mar 2019 22:30:22 +0000 Subject: [PATCH] Releasing 0.6.9 --- BioD | 2 +- INSTALL.md | 4 ++-- Makefile | 2 +- RELEASE-NOTES.md | 2 +- sambamba/main.d | 4 ++-- utils/version_.d | 2 +- 6 files changed, 8 insertions(+), 8 deletions(-) diff --git a/BioD b/BioD index 28ed6e38..23be3739 160000 --- a/BioD +++ b/BioD @@ -1 +1 @@ -Subproject commit 28ed6e382e178e8a8027d6bf2e5f9cc5884fc804 +Subproject commit 23be373986402ca65bfed0e6d0b23eacdd664601 diff --git a/INSTALL.md b/INSTALL.md index 31f6da63..a13c9fec 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -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 diff --git a/Makefile b/Makefile index 677146e6..5cb23b80 100644 --- a/Makefile +++ b/Makefile @@ -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 diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md index 4f6cee24..d6a0c319 100644 --- a/RELEASE-NOTES.md +++ b/RELEASE-NOTES.md @@ -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 diff --git a/sambamba/main.d b/sambamba/main.d index 99d5c71e..7bdb93b6 100644 --- a/sambamba/main.d +++ b/sambamba/main.d @@ -1,7 +1,7 @@ /* This file is part of Sambamba. Copyright (C) 2012-2017 Artem Tarasov - Copyright (C) 2012-2018 Pjotr Prins + Copyright (C) 2012-2019 Pjotr Prins 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(); diff --git a/utils/version_.d b/utils/version_.d index 2b3fa473..c1f2d04d 100644 --- a/utils/version_.d +++ b/utils/version_.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;