@@ -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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@@ -79,7 +79,7 @@ Sambamba is free and open source software, licensed under GPLv2+.
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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
@@ -90,7 +90,7 @@ are Github source and binary
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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
@@ -116,13 +116,12 @@ A [GNU Guix package](https://www.gnu.org/software/guix/packages/s.html) for samb
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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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-
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<a name =" help " ></a >
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# Getting help
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@@ -180,16 +179,7 @@ which targets LLVM. LLVM versions 6 is faster than earlier editions.
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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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@@ -224,6 +214,8 @@ you can run
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make check
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```
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+ See also [ INSTALL.md] ( ./INSTALL.md ) .
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+
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### GNU Guix
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To build sambamba the LDC compiler is also available in GNU Guix:
@@ -234,14 +226,13 @@ guix package -i ldc
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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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@@ -253,6 +244,7 @@ documentation can be found in the source code and the [development
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documentation] ( https://github.com/biod/sambamba-dev-docs ) .
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<a name =" debug " ></a >
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+
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# Debugging and troubleshooting
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## Segfaults on certain Intel Xeons
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