.gitmodules

@@ -7,6 +7,3 @@
 [submodule "BioD"]
 	path = BioD
 	url = https://github.com/biod/BioD.git
-[submodule "undeaD"]
-	path = undeaD
-	url = https://github.com/biod/undeaD.git

INSTALL.md

@@ -15,14 +15,20 @@
 After checking out the source from github with git submodules is is
 possibleto install the build tools with GNU Guix
 
-    guix package -i gcc gdb bash ld-wrapper ldc which python2 git
+    guix package -i gcc-toolchain 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-toolchain gdb bash ld-wrapper ldc which python git binutils-gold vim
     make clean
     make -j 4
     make check
 
 this way all dependencies are isolated.
+
+## Build Sambamba with Debian
+
+Make sure the environment is minimal with something like
+
+    env -i /bin/bash --login --noprofile --norc

Makefile

@@ -26,59 +26,61 @@ ifeq ($(UNAME_S),Darwin)
   SYS = OSX
 else
   SYS = LINUX
-  LINK_OBJ = utils/ldc_version_info_.o
 endif
 
-DFLAGS      = -wi -I. -IBioD -IundeaD/src -g
+DFLAGS      = -wi -I. -IBioD -g -J.
 
 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         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio2/*.d BioD/bio2/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
-OBJ         = $(SRC:.d=.o) utils/ldc_version_info_.o
-OUT         = bin/sambamba
+LIBS        = htslib/libhts.a lz4/lib/liblz4.a -L-L$(LIBRARY_PATH) -L-lpthread -L-lm -L-lz
+LIBS_STATIC = $(LIBRARY_PATH)/libc.a $(DLIBS) htslib/libhts.a $(LIBRARY_PATH)/liblz4.a -L-lz
+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         = $(SRC:.d=.o)
+OUT         = bin/sambamba-$(shell cat VERSION)
 
 STATIC_LIB_PATH=-Lhtslib -Llz4
 
 .PHONY: all debug release static clean test
 
+all: release
+
 debug:                             DFLAGS += -O0 -d-debug -link-debuglib
 
 profile:                           DFLAGS += -fprofile-instr-generate=profile.raw
 
-release static profile pgo-static: DFLAGS += -O3 -release -enable-inlining -boundscheck=off
+coverage:                          DFLAGS += -cov
+
+release static pgo-static:         DFLAGS += -O3 -release -enable-inlining -boundscheck=off -L-lz
 
 static:                            DFLAGS += -static -L-Bstatic
 
 pgo-static:                        DFLAGS += -fprofile-instr-use=profile.data
 
-all: release
-
 lz4-static: lz4/lib/liblz4.a
 
 lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c
 	cd lz4/lib && gcc -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && $(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o
 
 htslib-static:
-	cd htslib && $(MAKE)
+	cd htslib && $(MAKE) -j8
 
-ldc-version-info:
+utils/ldc_version_info_.d:
 	python3 ./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
 	cat utils/ldc_version_info_.d
 
-utils/ldc_version_info_.o: ldc-version-info
-	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)
+ldc_version_info: utils/ldc_version_info_.d
 
-build-setup: lz4-static htslib-static ldc-version-info
+build-setup: ldc_version_info lz4-static htslib-static
 	mkdir -p bin/
 
 default debug release static: $(OUT)
 
-profile: release
-	./bin/sambamba sort /gnu/data/in_raw.bam -p > /dev/null
+coverage: debug
+
+profile: debug
+	$(OUT) sort /gnu/data/in_raw.bam -p > /dev/null
 	ldc-profdata merge -output=profile.data profile.raw
-	rm ./bin/sambamba ./bin/sambamba.o # trigger rebuild
+	rm $(OUT) ./bin/sambamba.o # trigger rebuild
 
 default: all
 
@@ -86,17 +88,18 @@ default: all
 %.o: %.d
 	$(D_COMPILER) $(DFLAGS) -c $< -od=$(dir $@)
 
-singleobj:
+singleobj: build-setup
 	$(info compile single object...)
-	$(D_COMPILER) -singleobj $(DFLAGS) -c -of=bin/sambamba.o $(SRC)
+	$(D_COMPILER) -singleobj $(DFLAGS) -c -of=$(OUT).o $(SRC)
 
 # ---- Link step
-$(OUT): build-setup singleobj utils/ldc_version_info_.o
+$(OUT): singleobj
 	$(info linking...)
-	$(D_COMPILER) $(DFLAGS) -of=bin/sambamba bin/sambamba.o $(LINK_OBJ) $(LIBS)
+	$(D_COMPILER) $(DFLAGS) -of=$(OUT) $(OUT).o $(LINK_OBJ) $(LIBS)
 
-test:
-	./run_tests.sh
+test: $(OUT)
+	$(OUT) --version
+	./run_tests.sh $(OUT)
 
 check: test
 
@@ -106,16 +109,18 @@ debug-strip:
 	objcopy --add-gnu-debuglink=sambamba.debug bin/sambamba
 	mv sambamba.debug bin/
 
-pgo-static: profile static debug-strip
+pgo-static: static debug-strip
 
 install:
 	install -m 0755 bin/sambamba $(prefix)/bin
 
 clean: clean-d
 	cd htslib ; $(MAKE) clean
+	rm lz4/lib/*.[oa]
 	rm -f profile.data
 	rm -f profile.raw
 
 clean-d:
 	rm -rf bin/*
+	rm -vf utils/ldc_version_info_.d
 	rm -f $(OBJ) $(OUT) trace.{def,log}

Makefile.guix

 # GNU Guix makefile. GNU Guix is the package manager for GNU and we
 # use it for sambamba development and deployment. Normally use the
-# standard Makefile instead because it compiles into a singleobj.
+# standard Makefile instead because it compiles into a singleobj which
+# gives better performance. This Makefile is for development purposes.
 #
 # To build sambamba on GNU Guix:
 #
@@ -10,33 +11,30 @@
 #
 #   ./bin/sambamba
 #
-# certain paths may need to be set, e.g.
+# But it is preferred to run in a Guix environment/container. For more
+# information see INSTALL.md
 #
-#   make UNDEAD_PATH=../undeaD/src -f Makefile.guix
-#
-# For more information see INSTALL.md
-#
-# The following two are modified by the Guix package:
 D_COMPILER=ldc2
-ifndef GUIX
-  GUIX=$(HOME)/.guix-profile
-endif
-LDC_LIB_PATH=$(GUIX)/lib
+BIOD_PATH=./BioD
+
+# 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
 
-UNDEAD_PATH=../undeaD/src
-BIOD_PATH=../BioD
 
-DFLAGS = -wi -I. -I$(BIOD_PATH) -IundeaD/src -I$(UNDEAD_PATH)
+DFLAGS = -wi -I. -I$(BIOD_PATH) -J.
 # DLIBS  = $(LDC_LIB_PATH)/libphobos2-ldc.a $(LDC_LIB_PATH)/libdruntime-ldc.a
 # DLIBS_DEBUG = -debuglib=phobos2-ldc-debug,druntime-ldc-debug $(LDC_LIB_PATH)/libphobos2-ldc-debug.a $(LDC_LIB_PATH)/libdruntime-ldc-debug.a -link-debuglib
-DLIBS_DEBUG = -debuglib=phobos2-ldc-debug-shared,druntime-ldc-debug-shared -link-debuglib -L-lphobos2-ldc-debug-shared -L-ldruntime-ldc-debug-shared
-RPATH  = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $(LDC_LIB_PATH)/liblz4.so))
-LIBS   = htslib/libhts.a -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
+# DLIBS_DEBUG = -debuglib=phobos2-ldc-debug-shared,druntime-ldc-debug-shared -link-debuglib -L-lphobos2-ldc-debug-shared -L-ldruntime-ldc-debug-shared
+# RPATH  = -L--rpath=$(dir $(realpath $(LDC_LIB_PATH)/libz.so)):$(dir $(realpath $(LDC_LIB_PATH)/liblz4.so))
+RPATH = -L--rpath=$(LIBRARY_PATH)
+LIBS   = htslib/libhts.a -L-L$(LDC_LIB_PATH) -L-lrt -L-lpthread -L-lm -L-lz lz4/lib/liblz4.a
+
 # LIBS   = htslib/libhts.a -L-lrt -L-lpthread -L-lm -L-lz -L-llz4
-LIBS_STATIC = $(DLIBS) htslib/libhts.a $(LDC_LIB_PATH)/liblz4.a
-SRC         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.d) $(wildcard undeaD/src/undead/*.d undeaD/src/undead/*/*.d) $(wildcard BioD/bio/*/*.d BioD/bio/*/*/*.d BioD/bio2/*.d BioD/bio2/*/*.d) $(wildcard sambamba/*.d sambamba/*/*.d sambamba/*/*/*.d)
-OBJ    = $(SRC:.d=.o)
-OUT    = bin/sambamba
+LIBS_STATIC = $(DLIBS) htslib/libhts.a lz4/lib/liblz4.a
+SRC         = $(wildcard main.d utils/*.d thirdparty/*.d cram/*.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    = $(SRC:.d=.o) utils/ldc_version_info_.o
+OUT    = bin/sambamba-$(shell cat VERSION)
+static: OUT += -static
 
 .PHONY: all guix guix-debug debug release static profile clean test
 
@@ -46,17 +44,19 @@ guix:        DFLAGS += -O -release -g # Guix strips debug flags
 guix-debug:  DFLAGS += -O0 -g -d-debug -unittest
 
 # The following options are run in development from ~/.guix-profile and need to inject the RPATH
-debug:       DFLAGS += -O0 -g -d-debug $(RPATH) -link-debuglib -unittest
+debug:              DFLAGS += -O0 -g -d-debug $(RPATH) -link-debuglib -unittest
 
 release static:     DFLAGS += -O3 -release $(RPATH) -enable-inlining -Hkeep-all-bodies -boundscheck=off
 
-static:      DFLAGS += -static -L-Bstatic -L-L/gnu/store/rmjlycdgiq8pfy5hfi42qhw3k7p6kdav-glibc-2.25/lib/
+static:             DFLAGS += -static -L-Bstatic -L-L/gnu/store/rmjlycdgiq8pfy5hfi42qhw3k7p6kdav-glibc-2.25/lib/
+
+profile:            DFLAGS += -g -O -fprofile-instr-generate=profile.raw $(RPATH)
 
-profile:     DFLAGS += -g -O -profile $(RPATH)
+profile:            LIBS += -L=-lprofile_rt
 
-guix release:   LIBS += $(DLIBS)
+guix release:       LIBS += $(DLIBS)
 
-static:         LIBS = $(LIBS_STATIC)
+static:             LIBS = $(LIBS_STATIC)
 
 guix-debug debug profile: LIBS += $(DLIBS_DEBUG)
 
@@ -67,12 +67,25 @@ all: debug
 # sambamba/subsample.d: bio2/pileup.d
 
 utils/ldc_version_info_.d:
-	./gen_ldc_version_info.py $(shell which ldc2) > utils/ldc_version_info_.d
+	python3 ./gen_ldc_version_info.py $(shell which ldmd2) > utils/ldc_version_info_.d
+	cat utils/ldc_version_info_.d
+
+ldc_version_info: utils/ldc_version_info_.d
+
+lz4/lib/liblz4.a: lz4/lib/lz4.c lz4/lib/lz4hc.c lz4/lib/lz4frame.c lz4/lib/xxhash.c
+	cd lz4/lib && gcc -O3 -c lz4.c lz4hc.c lz4frame.c xxhash.c && $(AR) rcs liblz4.a lz4.o lz4hc.o lz4frame.o xxhash.o
+
+lz4-static: lz4/lib/liblz4.a
+
+build-setup: ldc_version_info lz4-static htslib-static
+	mkdir -p bin/
+
+# utils/ldc_version_info_.o: utils/ldc_version_info_.d
+# 	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)
 
-utils/ldc_version_info_.o: utils/ldc_version_info_.d
-	$(D_COMPILER) $(DFLAGS) -c utils/ldc_version_info_.d -od=$(dir $@)
+guix guix-debug default debug release static profile: ldc_version_info $(OUT)
 
-guix guix-debug default debug release static profile: $(OUT)
+debug profile release: lz4-static
 
 # ---- Compile step
 %.o: %.d
@@ -80,12 +93,12 @@ guix guix-debug default debug release static profile: $(OUT)
 
 # ---- Link step
 $(OUT): $(OBJ)
-	cd htslib && $(MAKE)
+	cd htslib && $(MAKE) -j 4
 	mkdir -p bin/
-	$(D_COMPILER) $(DFLAGS) -of=bin/sambamba $(OBJ) $(LIBS)
+	$(D_COMPILER) $(DFLAGS) -of=$(OUT) $(OBJ) $(LIBS)
 
 test:	clean-tests
-	./run_tests.sh
+	./run_tests.sh $(OUT)
 
 biod:
 	cd $(BIOD_PATH)/src_ragel && make
@@ -103,6 +116,7 @@ install:
 
 clean-c:
 	cd htslib ; make clean
+	rm -v lz4/lib/*.[oa]
 
 clean-d:
 	rm -v $(OBJ) $(OUT) trace.{def,log}
@@ -111,4 +125,4 @@ clean-d:
 clean-tests:
 	rm -rf output/*
 
-clean: clean-d clean-tests
+clean: clean-c clean-d clean-tests

README.md

-[![Build Status](https://travis-ci.org/biod/sambamba.svg?branch=master)](https://travis-ci.org/biod/sambamba) [![Anaconda-Server Badge](https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg)](https://conda.anaconda.org/bioconda) [![DL](https://anaconda.org/bioconda/sambamba/badges/downloads.svg)](https://anaconda.org/bioconda/sambamba)
+g[![Build Status](https://travis-ci.org/biod/sambamba.svg?branch=master)](https://travis-ci.org/biod/sambamba) [![AnacondaBadge](https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg)](https://anaconda.org/bioconda/sambamba) [![DL](https://anaconda.org/bioconda/sambamba/badges/downloads.svg)](https://anaconda.org/bioconda/sambamba) [![BrewBadge](https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg)](https://github.com/brewsci/homebrew-bio)
+[![GuixBadge](https://img.shields.io/badge/gnuguix-sambamba-brightgreen.svg)](https://www.gnu.org/software/guix/packages/S/)
+[![DebianBadge](https://badges.debian.net/badges/debian/testing/sambamba/version.svg)](https://packages.debian.org/testing/sambamba)
 
-# sambamba
+# SAMBAMBA
 
 Table of Contents
 =================
 
-   * [sambamba](#sambamba)
-      * [Table of Contents](#table-of-contents)
    * [Introduction](#introduction)
    * [Binary installation](#binary-installation)
       * [Install stable release](#install-stable-release)
@@ -38,41 +38,45 @@ Table of Contents
 
 Sambamba is a high performance highly parallel robust and fast tool
 (and library), written in the D programming language, for working with
-SAM and BAM files. Because of its efficiency is an important work
-horse running in many sequencing centres around the world
-today.
+SAM and BAM files. Because of its efficiency Sambamba is an important
+work horse running in many sequencing centres around the world today.
+As of November 2019, Sambamba has been cited over
+[277 times](http://scholar.google.nl/citations?hl=en&user=5ijHQRIAAAAJ)
+and has been installed from Conda over
+[120K times](https://anaconda.org/bioconda/sambamba).
 
 Current functionality is an important subset of samtools
 functionality, including view, index, sort, markdup, and depth. Most
 tools support piping: just specify `/dev/stdin` or `/dev/stdout` as
 filenames. When we started writing sambamba (in 2012) the main
 advantage over `samtools` was parallelized BAM reading and writing.
-In March 2017 `samtools` 1.4 was released, reaching parity on this. A
+In March 2017 `samtools` 1.4 was released, reaching parity at least on
+architecture. A
 [recent performance comparison](https://github.com/guigolab/sambamBench-nf)
-shows that sambamba holds its ground and can do better in different
-configurations. Here are some comparison
+shows that sambamba still holds its ground and can even do better.
+Here are some comparison
 [metrics](https://public-docs.crg.es/rguigo/Data/epalumbo/sambamba_ws_report.html). For
-example for flagstat sambamba is 1.4x faster than samtools. For index
+example, for flagstat sambamba is 1.4x faster than samtools. For index
 they are similar. For Markdup almost 6x faster and for view 4x
-faster. For sort sambamba has been beaten, though sambamba is up to 2x
-faster than samtools on large RAM machines (120GB+).
+faster. For sort sambamba has been beaten, though sambamba is notably
+up to 2x faster than samtools on large RAM machines (120GB+).
 
 In addition sambamba has a few interesting features to offer, in particular
 
-- faster large machine `sort`, see [performance](./test/benchmark/stats.org)
+- fast large machine `sort`, see [performance](./test/benchmark/stats.org)
 - automatic index creation when writing any coordinate-sorted file
 - `view -L <bed file>` utilizes BAM index to skip unrelated chunks
 - `depth` allows to measure base, sliding window, or region coverages
   - [Chanjo](https://www.chanjo.co/) builds upon this and gets you to exon/gene levels of abstraction
 - `markdup`, a fast implementation of Picard algorithm
 - `slice` quickly extracts a region into a new file, tweaking only first/last chunks
-- and more
+- and more (you'll have to try)
 
 Even though Sambamba started out as a samtools clone we are now in the
 process of adding new functionality - also in the
 [BioD project](https://github.com/biod/BioD). The D language is
-extremely suitable for high performance computing. At this point we
-think that the BAM format is here to stay for processing sequencing
+extremely suitable for high performance computing (HPC). At this point
+we think that the BAM format is here to stay for processing sequencing
 data and we aim to make it easy to parse and process BAM files.
 
 Sambamba is free and open source software, licensed under GPLv2+.
@@ -88,39 +92,42 @@ For more information on Sambamba contact the mailing list (see [Getting help](#g
 For those not in the mood to learn/install new package managers, there
 are Github source and binary
 [releases](https://github.com/biod/sambamba/releases). Simply download
-the tarball, unpack it and run it. For example
+the tarball, unpack it and run it according to the accompanying
+release notes.
 
-```bash
-wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba_v0.6.8_linux.tar.bz2
-tar xvjf sambamba_v0.6.8_linux.tar.bz2
-./sambamba_v0.6.8
-
-    sambamba 0.6.8
-
-        Usage: sambamba [command] [args...]
-
-        Available commands: 'view', 'index', 'merge', 'sort',
-                             'flagstat', 'slice', 'markdup', 'depth', 'mpileup'
-        To get help on a particular command, just call it without args.
-```
+Below package managers Conda, GNU Guix, Debian and Homebrew also
+provide recent binary installs for Linux.  For MacOS you may use Conda
+or Homebrew.
 
 ## Bioconda install
 
 [![Install with CONDA](https://anaconda.org/bioconda/sambamba/badges/installer/conda.svg)](https://anaconda.org/bioconda/sambamba)
 
+Ther should be binary downloads for Linux and MacOS.
+
 With Conda use the [`bioconda`](https://bioconda.github.io/) channel.
 
 ## GNU Guix install
 
-A [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for sambamba is available. The development version is packaged [here](https://gitlab.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/sambamba.scm).
+[![GuixBadge](https://img.shields.io/badge/gnuguix-sambamba--0.6.8-brightgreen.svg)](https://www.gnu.org/software/guix/packages/S/)
+
+A reproducible [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for sambamba is available. The development version is packaged [here](https://gitlab.com/genenetwork/guix-bioinformatics/blob/master/gn/packages/sambamba.scm).
 
 ## Debian GNU/Linux install
 
-Debian: see [Debian packages](https://tracker.debian.org/pkg/sambamba).
+[![DebianBadge](https://badges.debian.net/badges/debian/testing/sambamba/version.svg)](https://packages.debian.org/testing/sambamba)
+
+See also Debian package [status](https://tracker.debian.org/pkg/sambamba).
 
 ## Homebrew install
 
-Users of Homebrew can also use the formula from `homebrew-science`.
+[![BrewBadge](https://img.shields.io/badge/%F0%9F%8D%BAbrew-sambamba-brightgreen.svg)](https://github.com/brewsci/homebrew-bio)
+
+Users of Homebrew can also use the formula from [homebrew-bio](https://github.com/brewsci/homebrew-bio).
+
+    brew install brewsci/bio/sambamba
+
+It should work for Linux and MacOS.
 
 <a name="help"></a>
 # Getting help
@@ -284,7 +291,8 @@ command). A full stacktrace for all threads:
 thread apply all backtrace full
 ```
 
-Note that GDB should be made aware of D garbage collector:
+Note that GDB should be made aware of D garbage collector which emits
+SIGUSR signals and gdb needs to ignore them with
 
 ```
 handle SIGUSR1 SIGUSR2 nostop noprint
@@ -308,13 +316,14 @@ gdb -ex 'handle SIGUSR1 SIGUSR2 nostop noprint' \
 <a name="license"></a>
 # License
 
-Sambamba is distributed under GNU Public License v2+.
+Sambamba is generously distributed under GNU Public License v2+.
 
 <a name="credits"></a>
 # Credit
 
-If you are using Sambamba in your research and want to support future
-work on Sambamba, please cite the following publication:
+Citations are the bread and butter of Science.  If you are using
+Sambamba in your research and want to support our future work on
+Sambamba, please cite the following publication:
 
 A. Tarasov, A. J. Vilella, E. Cuppen, I. J. Nijman, and P. Prins. [Sambamba: fast processing of NGS alignment formats](https://doi.org/10.1093/bioinformatics/btv098). Bioinformatics, 2015.
 

RELEASE-NOTES.md

+## ChangeLog v0.7.1 (20191128)
+
++ Fixed major segfault problem that got introduced after ldc 1.10, see https://github.com/biod/sambamba/issues/393
++ make error message more informative - see https://github.com/biod/sambamba/pull/411/files, thanks https://github.com/EwaMarek
+
+## ChangeLog v0.7.0 (20190529)
+
++ Release avoids crashing problem by building with ldc-1.10.0, see https://github.com/biod/sambamba/issues/393
++ Merge pull request #396 from joelmartin/flagstat-return returning 0
+
+## 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
++ Many module renames to build a BioD for the future - thanks https://github.com/george-githinji
+
 ## ChangeLog v0.6.8 (20181004)
 
 Pre-release with a much faster statically compiled binary. 10-20%
@@ -33,7 +49,7 @@ To install the image, download and
 
 ```sh
 md5sum sambamba-0.6.8.gz
-25efb5604ae5fe7c750e8020326787c5  sambamba-0.8.6.gz
+ee61000bcb33a82013c284bac8feb91f  sambamba-0.6.8.gz
 gzip -d sambamba-0.6.8.gz
 chmod a+x sambamba-0.6.8
 
@@ -43,7 +59,7 @@ sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
     LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
 ```
 
-The binary images were reproducibly built on x86_64 with
+The binary images were built on x86_64 with
 
 ```sh
 ~/.config/guix/current/bin/guix pull -l
@@ -53,7 +69,6 @@ Generation 3    Sep 25 2018 09:39:08
     branch: origin/master
     commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
 
-
 guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
 make clean && make -j 16 && make check
 
@@ -65,7 +80,7 @@ for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
 /gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1
 /gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so
 # build static image
-make clean && make release -j 16 && make check
+make clean && make static -j 16 && make check
 ```
 
 Git submodule versions were

VERSION

+0.7.1

cram/reader.d

@@ -8,8 +8,8 @@ import cram.exception;
 import cram.wrappers;
 import cram.slicereader;
 
-import bio.bam.abstractreader, bio.bam.referenceinfo,
-       bio.sam.header, bio.bam.reference, bio.bam.read;
+import bio.std.hts.bam.abstractreader, bio.std.hts.bam.referenceinfo,
+       bio.std.hts.sam.header, bio.std.hts.bam.reference, bio.std.hts.bam.read;
 import std.string, std.array, std.range, std.algorithm, std.conv, std.typecons;
 import std.parallelism;
 
@@ -108,7 +108,7 @@ class CramReader : IBamSamReader {
         return reads;
     }
 
-    std.range.InputRange!(bio.bam.read.BamRead) allReads() @property {
+    std.range.InputRange!(bio.std.hts.bam.read.BamRead) allReads() @property {
         return inputRangeObject(reads());
     }
 

cram/reference.d

@@ -3,9 +3,9 @@ module cram.reference;
 import cram.exception, cram.wrappers, cram.slicereader;
 import cram.htslib;
 
-import bio.bam.abstractreader;
-import bio.bam.referenceinfo;
-import bio.bam.read;
+import bio.std.hts.bam.abstractreader;
+import bio.std.hts.bam.referenceinfo;
+import bio.std.hts.bam.read;
 import std.string;
 import std.parallelism;
 import std.range, std.algorithm;

cram/slicereader.d

 module cram.slicereader;
 
 import cram.htslib, cram.wrappers, cram.exception;
-import bio.bam.abstractreader, bio.bam.read;
+import bio.std.hts.bam.abstractreader, bio.std.hts.bam.read;
 
 alias AllocateFunc = ubyte[] function(size_t);
 

cram/writer.d

 module cram.writer;
 
-import undead.stream;
+import contrib.undead.stream;
 import std.string;
 
 import cram.htslib;
 import cram.exception;
 
-import bio.bam.read;
-import bio.bam.referenceinfo;
-import bio.sam.header;
+import bio.std.hts.bam.read;
+import bio.std.hts.bam.referenceinfo;
+import bio.std.hts.sam.header;
 
 extern(C) {
     int fai_build(const(char)* fn);

debian/changelog

-sambamba (0.6.8-1) UNRELEASED; urgency=medium
+sambamba (0.7.1-1) unstable; urgency=medium
 
+  [ Andreas Tille ]
   * New upstream release
     Closes: #907489
   * Point Vcs fields to salsa.debian.org
@@ -8,7 +9,25 @@ sambamba (0.6.8-1) UNRELEASED; urgency=medium
   * Allow pre-releases in watch file
   * Versioned Build-Depends: libbiod (>= 0.2.1)
 
- -- Andreas Tille <tille@debian.org>  Thu, 04 Oct 2018 10:06:08 +0200
+  [ Steffen Möller ]
+  * Update metadata with ref to conda
+
+  [ Matthias Klumpp ]
+  * New upstream version: 0.7.1
+  * Run tests and build with strong optimizations
+  * add-meson-build.patch: Update Meson build definition
+    - Closes: #907489
+    - We link against BioD stantically now
+    - Tests are integrated into Meson
+    - Allow switching on stronger optimizations used by the
+      upstream Makefile
+  * Depend on latest libbiod (>= 0.2.3)
+  * Don't depend on libundead
+  * Bump dh compat level to 12
+  * Bump standards version (No changes needed)
+  * Remove test artifacts in clean target
+
+ -- Matthias Klumpp <mak@debian.org>  Sun, 15 Dec 2019 12:52:42 +0100
 
 sambamba (0.6.7-2) unstable; urgency=medium
 

debian/compat

-11

debian/control

@@ -3,18 +3,17 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-dlang,
-               libbiod-dev (>= 0.2.1),
+               libbiod-dev (>= 0.2.3),
                libhts-dev,
                liblz4-dev,
-               libundead-dev,
-               meson (>= 0.40),
+               meson (>= 0.48),
                pkg-config,
                python,
-               zlib1g-dev,
-               shunit2
-Standards-Version: 4.2.1
+               shunit2,
+               zlib1g-dev
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/sambamba
 Vcs-Git: https://salsa.debian.org/med-team/sambamba.git
 Homepage: https://github.com/lomereiter/sambamba

debian/copyright

@@ -13,4 +13,3 @@ License: GPL-2+
 License: GPL-2+
  On Debian systems you can find the full text of the GNU General Public
  License version 2 or later at /usr/share/common-licenses/GPL-2.
- 
\ No newline at end of file

debian/patches/01_add_meson.patch → debian/patches/01_add-meson-build.patch

-From 8a7812717d7810355786219a250671539b933e0f Mon Sep 17 00:00:00 2001
+From 61437f3f44ced71436b366f1789fb5ee4e3cabeb Mon Sep 17 00:00:00 2001
 From: Matthias Klumpp <matthias@tenstral.net>
-Date: Sun, 30 Apr 2017 17:41:14 +0200
-Subject: [PATCH] Add Meson build file
+Date: Sun, 15 Dec 2019 02:24:44 +0100
+Subject: [PATCH] Add Meson build definition
 
 ---
- meson.build | 135 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
- 1 file changed, 135 insertions(+)
+ .gitignore        |   1 +
+ meson.build       | 141 ++++++++++++++++++++++++++++++++++++++++++++++
+ meson_options.txt |   1 +
+ 3 files changed, 143 insertions(+)
  create mode 100644 meson.build
+ create mode 100644 meson_options.txt
 
+diff --git a/.gitignore b/.gitignore
+index 7062b3a..a6cbb18 100644
+--- a/.gitignore
++++ b/.gitignore
+@@ -16,6 +16,7 @@ shunit*
+ /*.cram
+ /*.crai
+ /*.txt
++!meson_options.txt
+ *.hex
+ *.zcat
+ *.out
+diff --git a/meson.build b/meson.build
+new file mode 100644
+index 0000000..3dd9cde
 --- /dev/null
 +++ b/meson.build
-@@ -0,0 +1,138 @@
-+project('Sambamba', 'd')
-+
-+project_version   = '0.6.6'
+@@ -0,0 +1,141 @@
++project('Sambamba', 'd',
++    meson_version : '>=0.48',
++    license : 'GPL-2.0',
++    version : '0.7.1',
++    default_options : ['buildtype=debugoptimized']
++)
 +
 +source_root = meson.source_root()
 +build_root = meson.build_root()
 +
++# we need a C compiler for the static library search (for BioD) to work,
++# as the D compiler abstraction in Meson doesn't have find_library() capabilities yet
++add_languages('c')
++
 +if meson.get_compiler('d').get_id() != 'llvm'
-+    error('We only support the LLVm D compiler at time. Please compile with LDC.')
++    error('We only support the LLVM D compiler at time. Please compile with LDC.')
++endif
++extra_dflags = []
++if get_option('optimize_strong')
++    extra_dflags = ['-O3', '-release', '-enable-inlining', '-boundscheck=off']
 +endif
 +
 +#
@@ -30,14 +59,13 @@ Subject: [PATCH] Add Meson build file
 +    'sambamba/fixbins.d',
 +    'sambamba/flagstat.d',
 +    'sambamba/index.d',
-+    'sambamba/markdup.d',
 +    'sambamba/markdup2.d',
++    'sambamba/markdup.d',
 +    'sambamba/merge.d',
 +    'sambamba/pileup.d',
 +    'sambamba/slice.d',
 +    'sambamba/sort.d',
 +    'sambamba/subsample.d',
-+    'sambamba/validate.d',
 +    'sambamba/utils/common/bed.d',
 +    'sambamba/utils/common/file.d',
 +    'sambamba/utils/common/filtering.d',
@@ -51,7 +79,8 @@ Subject: [PATCH] Add Meson build file
 +    'sambamba/utils/common/tmpdir.d',
 +    'sambamba/utils/view/alignmentrangeprocessor.d',
 +    'sambamba/utils/view/headerserializer.d',
-+    'sambamba/view.d'
++    'sambamba/validate.d',
++    'sambamba/view.d',
 +]
 +
 +utils_src = [
@@ -90,12 +119,10 @@ Subject: [PATCH] Add Meson build file
 +#
 +# Dependencies
 +#
-+undead_dep = dependency('undead', version: '>=1.0.6')
-+biod_dep   = dependency('biod', version: '>=0.1.0')
++biod_dep   = dependency('biod', version: '>=0.1.0', static: true)
 +lz4_dep    = dependency('liblz4')
 +htslib_dep = dependency('htslib', version: '>=1.3.2')
 +
-+
 +#
 +# Configure
 +#
@@ -123,29 +150,30 @@ Subject: [PATCH] Add Meson build file
 +     cram_src,
 +     thirdparty_src,
 +     version_info_d_fname],
-+    dependencies: [undead_dep,
-+                   biod_dep,
++    dependencies: [biod_dep,
 +                   lz4_dep,
 +                   htslib_dep],
++    d_args: extra_dflags,
++    d_import_dirs: [include_directories('.')],
 +    install: true
 +)
 +
-+sambamba_test_exe = executable('sambamba_test',
-+    [sambamba_src,
-+     utils_src,
-+     cram_src,
-+     thirdparty_src],
-+    dependencies: [undead_dep,
-+                   biod_dep,
-+                   lz4_dep,
-+                   htslib_dep],
-+    d_args: meson.get_compiler('d').unittest_args(),
-+    link_args: '-main'
++test_exe = find_program(join_paths(source_root, 'test', 'test_suite.sh'))
++test('sambamba_test',
++     test_exe,
++     env: ['sambamba=' + sambamba_exe.full_path()],
++     workdir: source_root
 +)
 +
 +#
 +# Install extra files
 +#
-+
 +install_man(manpages)
 +install_data(['etc/bash_completion.d/sambamba'], install_dir: '/usr/share/bash-completion/completions')
+diff --git a/meson_options.txt b/meson_options.txt
+new file mode 100644
+index 0000000..607da9a
+--- /dev/null
++++ b/meson_options.txt
+@@ -0,0 +1 @@
++option('optimize_strong', type : 'boolean', value: false)

debian/patches/series

-01_add_meson.patch
-disable-assert.patch
+01_add-meson-build.patch
+02_disable-assert.patch

debian/rules

 #!/usr/bin/make -f
 # DH_VERBOSE := 1
 
-export DEB_BUILD_MAINT_OPTIONS=hardening=+all
-
 include /usr/share/dh-dlang/dlang-flags.mk
 
 %:
 	dh $@ --buildsystem=meson
 
-override_dh_auto_test:
-ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-	./run_tests.sh
-endif
+override_dh_auto_configure:
+	dh_auto_configure -- -Doptimize_strong=true
 
-override_missing:
+override_dh_missing:
 	dh_missing --fail-missing
+
+override_dh_auto_clean:
+	dh_auto_clean
+	-rm -r $(CURDIR)/output/

doc/design.org

@@ -12,6 +12,9 @@ example, see this [[http://forum.dlang.org/thread/gvtjhpxdqpboppoodmxm@forum.dla
 carefully, suggests we should use multiple implementations for file
 access.
 
+The current version for sambamba is much loved for markdup, depth and
+slice options. It is logical to revisit these.
+
 Here we document some of the choices we are making for the new
 design. Starting with markdup2, the new version is a prototype for new
 sambamba architecture using more canonical D language features,
@@ -71,3 +74,9 @@ should use that.
 
 Because of the pipes it is crucial sambamba gives clear error messages
 and should be capable of writing to a log file.
+
+* Markdup
+
+The original markdup routine is written in sambamba/markdup.d. It
+maintains state in a structure called IndexedBamRead with an index
+value and the read object.