diff --git a/AUTHORS b/AUTHORS index 32fe374..c60b6cb 100644 --- a/AUTHORS +++ b/AUTHORS @@ -4,16 +4,15 @@ Primary contact Ben Langmead and Cole Trapnell wrote Bowtie. The SeqAn-1.1 library is used in Bowtie and some of its sources are included in Bowtie source releases; its authors are Andreas Doring, David Weese, Tobias Rausch, -and Knut Reinert. A DLL from the pthreads for Win32 library is -distributed with the Win32 version of Bowtie. The pthreads for Win32 -library and the GnuWin32 package have many contributors (see their -respective web sites). +and Knut Reinert. The tinythreads library has been written by Marcus Geelnard. +The pthreads for Win32 library and the GnuWin32 package have many contributors +(see their respective web sites). Websites: Bowtie: http://bowtie-bio.sf.net SeqAn: http://www.seqan.de - pthreads for Win32: http://sourceware.org/pthreads-win32 GnuWin32: http://gnuwin32.sf.net + tinythreads: http://tinythreadpp.bitsnbites.eu/ December 2009 diff --git a/MANUAL b/MANUAL index cb142a0..574982d 100644 --- a/MANUAL +++ b/MANUAL @@ -78,8 +78,11 @@ sometimes with `gmake`) with no arguments. If building with [MinGW], run `make` from the [MSYS] command line. To support the `-p` (multithreading) option, Bowtie needs the -`pthreads` library. To compile Bowtie without `pthreads` (which -disables `-p`), use `make BOWTIE_PTHREADS=0`. +`pthreads` library on posix platforms like linux or will try to +use native Win32 threads on Windows. For threading synchronization +bowtie is using by default a spinlocking mechanism. Spinlocking is +in general much faster. However if the need arise to not use spinlocking +bowtie can also be compiled using EXTRA_FLAGS=-DNO_SPINLOCK parameter. [Cygwin]: http://www.cygwin.com/ [MinGW]: http://www.mingw.org/ @@ -1576,11 +1579,6 @@ architectures). Use `` as the seed for pseudo-random number generator. - --cutoff - -Index only the first `` bases of the reference sequences -(cumulative across sequences) and ignore the rest. - -q/--quiet `bowtie-build` is verbose by default. With this option `bowtie-build` diff --git a/MANUAL.markdown b/MANUAL.markdown index c064ed9..3ca7d20 100644 --- a/MANUAL.markdown +++ b/MANUAL.markdown @@ -83,8 +83,11 @@ sometimes with `gmake`) with no arguments. If building with [MinGW], run `make` from the [MSYS] command line. To support the [`-p`] (multithreading) option, Bowtie needs the -`pthreads` library. To compile Bowtie without `pthreads` (which -disables [`-p`]), use `make BOWTIE_PTHREADS=0`. +`pthreads` library on posix platforms like linux or will try to +use native Win32 threads on Windows. For threading synchronization +bowtie is using by default a spinlocking mechanism. Spinlocking is +in general much faster. However if the need arise to not use spinlocking +bowtie can also be compiled using EXTRA_FLAGS=-DNO_SPINLOCK parameter. [Cygwin]: http://www.cygwin.com/ [MinGW]: http://www.mingw.org/ diff --git a/doc/manual.html b/doc/manual.html index e50240a..6a1e5ea 100644 --- a/doc/manual.html +++ b/doc/manual.html @@ -87,7 +87,7 @@

Obtaining Bowtie

Building from source

Building Bowtie from source requires a GNU-like environment that includes GCC, GNU Make and other basics. It should be possible to build Bowtie on a vanilla Linux or Mac installation. Bowtie can also be built on Windows using Cygwin or MinGW. We recommend TDM's MinGW Build. If using MinGW, you must also have MSYS installed.

To build Bowtie, extract the sources, change to the extracted directory, and run GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS command line.

-

To support the -p (multithreading) option, Bowtie needs the pthreads library. To compile Bowtie without pthreads (which disables -p), use make BOWTIE_PTHREADS=0.

+

To support the -p (multithreading) option, Bowtie needs the pthreads library on posix platforms like linux or will try to use native Win32 threads on Windows. For threading synchronization bowtie is using by default a spinlocking mechanism. Spinlocking is in general much faster. However if the need arise to not use spinlocking bowtie can also be compiled using EXTRA_FLAGS=-DNO_SPINLOCK parameter.

The bowtie aligner

bowtie takes an index and a set of reads as input and outputs a list of alignments. Alignments are selected according to a combination of the -v/-n/-e/-l options (plus the -I/-X/--fr/--rf/ --ff options for paired-end alignment), which define which alignments are legal, and the -k/-a/-m/-M/--best/--strata options which define which and how many legal alignments should be reported.

By default, Bowtie enforces an alignment policy similar to Maq's default quality-aware policy (-n 2 -l 28 -e 70). See the -n alignment mode section of the manual for details about this mode. But Bowtie can also enforce a simpler end-to-end k-difference policy (e.g. with -v 2). See the -v alignment mode section of the manual for details about that mode. The -n alignment mode and the -v alignment mode are mutually exclusive.

@@ -1092,12 +1092,6 @@

Options

Use <int> as the seed for pseudo-random number generator.

-
--cutoff <int>
- - -

Index only the first <int> bases of the reference sequences (cumulative across sequences) and ignore the rest.

- - 
-q/--quiet
diff --git a/doc/website/manual.ssi b/doc/website/manual.ssi index 55b6340..ccc4911 100644 --- a/doc/website/manual.ssi +++ b/doc/website/manual.ssi @@ -1,5 +1,5 @@

Table of Contents

-

Bowtie 0.12.9

+

Bowtie 1.0.0

    @@ -79,7 +79,7 @@

    Building from source

    Building Bowtie from source requires a GNU-like environment that includes GCC, GNU Make and other basics. It should be possible to build Bowtie on a vanilla Linux or Mac installation. Bowtie can also be built on Windows using Cygwin or MinGW. We recommend TDM's MinGW Build. If using MinGW, you must also have MSYS installed.

    To build Bowtie, extract the sources, change to the extracted directory, and run GNU make (usually with the command make, but sometimes with gmake) with no arguments. If building with MinGW, run make from the MSYS command line.

    -

    To support the -p (multithreading) option, Bowtie needs the pthreads library. To compile Bowtie without pthreads (which disables -p), use make BOWTIE_PTHREADS=0.

    +

    To support the -p (multithreading) option, Bowtie needs the pthreads library on posix platforms like linux or will try to use native Win32 threads on Windows. For threading synchronization bowtie is using by default a spinlocking mechanism. Spinlocking is in general much faster. However if the need arise to not use spinlocking bowtie can also be compiled using EXTRA_FLAGS=-DNO_SPINLOCK parameter.

    The bowtie aligner

    bowtie takes an index and a set of reads as input and outputs a list of alignments. Alignments are selected according to a combination of the -v/-n/-e/-l options (plus the -I/-X/--fr/--rf/ --ff options for paired-end alignment), which define which alignments are legal, and the -k/-a/-m/-M/--best/--strata options which define which and how many legal alignments should be reported.

    By default, Bowtie enforces an alignment policy similar to Maq's default quality-aware policy (-n 2 -l 28 -e 70). See the -n alignment mode section of the manual for details about this mode. But Bowtie can also enforce a simpler end-to-end k-difference policy (e.g. with -v 2). See the -v alignment mode section of the manual for details about that mode. The -n alignment mode and the -v alignment mode are mutually exclusive.

    @@ -1084,12 +1084,6 @@ T2302111203131231130300111123220

    Use <int> as the seed for pseudo-random number generator.

    -
    --cutoff <int>
    - - -

    Index only the first <int> bases of the reference sequences (cumulative across sequences) and ignore the rest.

    - - 
    -q/--quiet