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Release v0.8.6
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README.md

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@@ -54,8 +54,8 @@ configurations. Here are some comparison
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[metrics](https://public-docs.crg.es/rguigo/Data/epalumbo/sambamba_ws_report.html). For
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example for flagstat sambamba is 1.4x faster than samtools. For index
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they are similar. For Markdup almost 6x faster and for view 4x
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faster. For sort sambamba has been beaten generally, though sambamba
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is up to 2x faster on large RAM machines.
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faster. For sort sambamba has been beaten, though sambamba is up to 2x
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faster than samtools on large RAM machines (120GB+).
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In addition sambamba has a few interesting features to offer, in particular
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See manual pages [online](https://lomereiter.github.io/sambamba/docs/sambamba-view.html)
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to know more about what is available and how to use it.
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For more information on Sambamba contact the mailing list (see below).
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For more information on Sambamba contact the mailing list (see [Getting help](#getting-help)).
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<a name="install"></a>
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# Binary installation
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[releases](https://github.com/biod/sambamba/releases). Simply download
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the tarball, unpack it and run it. For example
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```sh
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```bash
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wget https://github.com/biod/sambamba/releases/download/v0.6.8/sambamba_v0.6.8_linux.tar.bz2
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tar xvjf sambamba_v0.6.8_linux.tar.bz2
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./sambamba_v0.6.8
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## Debian GNU/Linux install
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Debian: see Debian packages.
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Debian: see [Debian packages](https://tracker.debian.org/pkg/sambamba).
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## Homebrew install
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Users of Homebrew can also use the formula from `homebrew-science`.
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<a name="help"></a>
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# Getting help
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## Compilation dependencies
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- git (to check out the repo)
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- gcc compiler 4.9 or later (for htslib)
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- D compiler 1.7.0 or later (ldc2, see below)
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- python2 (parses D-compiler header for version info)
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- zlib (library)
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- lz4 (library)
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- htslib (submodule)
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- BioD (source)
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- undeaD (source)
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- python2
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See [INSTALL.md](./INSTALL.md).
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## Compiling for Linux
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make check
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```
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See also [INSTALL.md](./INSTALL.md).
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### GNU Guix
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To build sambamba the LDC compiler is also available in GNU Guix:
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## Compiling for Mac OS X
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Note: the Makefile does not work. Someone want to fix that using the
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Makefile.old version? See also https://github.com/biod/sambamba/issues/338.
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Sambamba builds on MacOS. We have a Travis [integration test](https://travis-ci.org/pjotrp/sambamba) as
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an example. It can be something like
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```sh
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brew install ldc
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git clone --recursive https://github.com/biod/sambamba.git
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cd sambamba
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git clone https://github.com/dlang/undeaD
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make
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```
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documentation](https://github.com/biod/sambamba-dev-docs).
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<a name="debug"></a>
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# Debugging and troubleshooting
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## Segfaults on certain Intel Xeons

RELEASE-NOTES.md

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## ChangeLog v0.6.8 (20181003)
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## ChangeLog v0.6.8 (20181004)
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Pre-release with a much faster statically compiled binary. 10-20%
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faster than v0.6.6, due to ldc and LLVM improvements. Fixes speed
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regression of v0.6.7 for large files due to singleobj compilation. See
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also #345 and
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[performance](https://github.com/biod/sambamba/blob/master/test/benchmark/stats.org)
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64-bit compilation should be fine on ldc 1.10. i386 target is still a problem.
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64-bit compilation should be fine on ldc 1.10+. i386 target is still a problem.
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+ Fix mark duplicates in files with many contigs, see #361 (thanks Devon Ryan @dpryan79)
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+ Fix missing PM tag in #356 (thanks Kurt Hetrick @Kurt-Hetrick)
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+ Added shunit2 to the source tree for testing
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+ Update python build dependencies to use python3.x
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+ Fixed a number of D compiler messages on deprecated features (ldc 1.11)
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To install the image, download and
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```sh
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md5sum sambamba-0.6.8.gz
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25efb5604ae5fe7c750e8020326787c5 sambamba-0.8.6.gz
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gzip -d sambamba-0.6.8.gz
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chmod a+x sambamba-0.6.8
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./sambamba-0.8.6
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sambamba 0.6.8 by Artem Tarasov and Pjotr Prins (C) 2012-2018
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LDC 1.10.0 / DMD v2.080.1 / LLVM6.0.1 / bootstrap LDC - the LLVM D compiler (0.17.4)
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```
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The binary images were reproducibly built on x86_64 with
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```sh
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~/.config/guix/current/bin/guix pull -l
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Generation 3 Sep 25 2018 09:39:08
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guix 932839f
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repository URL: https://git.savannah.gnu.org/git/guix.git
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branch: origin/master
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commit: 932839ff124ff3b0dd3070914fb1c5beec69bf32
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guix environment -C guix --ad-hoc gcc gdb bash ld-wrapper ldc which python git
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make clean && make -j 16 && make check
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for x in `ldd bin/sambamba|cut -d ' ' -f 3` ; do realpath $x ; done
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/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libpthread-2.27.so
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/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libm-2.27.so
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/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/librt-2.27.so
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/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libdl-2.27.so
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/gnu/store/bmaxmigwnlbdpls20px2ipq1fll36ncd-gcc-8.2.0-lib/lib/libgcc_s.so.1
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/gnu/store/l4lr0f5cjd0nbsaaf8b5dmcw1a1yypr3-glibc-2.27/lib/libc-2.27.so
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# build static image
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make clean && make release -j 16 && make check
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```
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Git submodule versions were
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```
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git submodule status
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2f0634b187e0f454809432093238cf31e9fbfee6 BioD (v0.2.0-5-g2f0634b)
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2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5 htslib (0.2.0-rc10-271-g2f3c3ea)
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b3692db46d2b23a7c0af2d5e69988c94f126e10a lz4 (v1.8.2)
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9be93876982b5f14fcca60832563b3cd767dd84d undeaD (v1.0.1-49-g9be9387)
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```

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