Updates for v1.0.0 release

AUTHORS

@@ -4,16 +4,15 @@ Primary contact <blangmea@jhsph.edu>
 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

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 `<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
 
 `bowtie-build` is verbose by default.  With this option `bowtie-build`

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/

doc/manual.html

@@ -87,7 +87,7 @@ <h1 id="obtaining-bowtie"><a href="#TOC">Obtaining Bowtie</a></h1>
 <h2 id="building-from-source"><a href="#TOC">Building from source</a></h2>
 <p>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 <a href="http://www.cygwin.com/">Cygwin</a> or <a href="http://www.mingw.org/">MinGW</a>. We recommend <a href="http://www.tdragon.net/recentgcc/">TDM's MinGW Build</a>. If using <a href="http://www.mingw.org/">MinGW</a>, you must also have <a href="http://www.mingw.org/wiki/msys">MSYS</a> installed.</p>
 <p>To build Bowtie, extract the sources, change to the extracted directory, and run GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with <a href="http://www.mingw.org/">MinGW</a>, run <code>make</code> from the <a href="http://www.mingw.org/wiki/msys">MSYS</a> command line.</p>
-<p>To support the <a href="#bowtie-options-p"><code>-p</code></a> (multithreading) option, Bowtie needs the <code>pthreads</code> library. To compile Bowtie without <code>pthreads</code> (which disables <a href="#bowtie-options-p"><code>-p</code></a>), use <code>make BOWTIE_PTHREADS=0</code>.</p>
+<p>To support the <a href="#bowtie-options-p"><code>-p</code></a> (multithreading) option, Bowtie needs the <code>pthreads</code> 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.</p>
 <h1 id="the-bowtie-aligner"><a href="#TOC">The <code>bowtie</code> aligner</a></h1>
 <p><code>bowtie</code> 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 <a href="#bowtie-options-v"><code>-v</code></a>/<a href="#bowtie-options-n"><code>-n</code></a>/<a href="#bowtie-options-e"><code>-e</code></a>/<a href="#bowtie-options-l"><code>-l</code></a> options (plus the <a href="#bowtie-options-I"><code>-I</code></a>/<a href="#bowtie-options-X"><code>-X</code></a>/<a href="#bowtie-options-fr"><code>--fr</code></a>/<a href="#bowtie-options-fr"><code>--rf</code></a>/ <a href="#bowtie-options-fr"><code>--ff</code></a> options for paired-end alignment), which define which alignments are legal, and the <a href="#bowtie-options-k"><code>-k</code></a>/<a href="#bowtie-options-a"><code>-a</code></a>/<a href="#bowtie-options-m"><code>-m</code></a>/<a href="#bowtie-options-m"><code>-M</code></a>/<a href="#bowtie-options-best"><code>--best</code></a>/<a href="#bowtie-options-strata"><code>--strata</code></a> options which define which and how many legal alignments should be reported.</p>
 <p>By default, Bowtie enforces an alignment policy similar to <a href="http://maq.sf.net">Maq</a>'s default quality-aware policy (<a href="#bowtie-options-n"><code>-n</code></a> 2 <a href="#bowtie-options-l"><code>-l</code></a> 28 <a href="#bowtie-options-e"><code>-e</code></a> 70). See <a href="#the--n-alignment-mode">the -n alignment mode</a> 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 <a href="#bowtie-options-v"><code>-v</code></a> 2). See <a href="#the--v-alignment-mode">the -v alignment mode</a> section of the manual for details about that mode. <a href="#the--n-alignment-mode">The -n alignment mode</a> and <a href="#the--v-alignment-mode">the -v alignment mode</a> are mutually exclusive.</p>
@@ -1092,12 +1092,6 @@ <h3 id="options-1"><a href="#TOC">Options</a></h3>
 <p>Use <code>&lt;int&gt;</code> as the seed for pseudo-random number generator.</p>
 </td></tr><tr><td>
 
-<pre><code>--cutoff &lt;int&gt;</code></pre>
-</td><td>
-
-<p>Index only the first <code>&lt;int&gt;</code> bases of the reference sequences (cumulative across sequences) and ignore the rest.</p>
-</td></tr><tr><td>
-
 <pre><code>-q/--quiet</code></pre>
 </td><td>
 

doc/website/manual.ssi

@@ -1,5 +1,5 @@
 <h1>Table of Contents</h1>
-<p>Bowtie 0.12.9</p>
+<p>Bowtie 1.0.0</p>
 
 <div id="TOC">
 <ul>
@@ -79,7 +79,7 @@
 <h2 id="building-from-source"><a href="#TOC">Building from source</a></h2>
 <p>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 <a href="http://www.cygwin.com/">Cygwin</a> or <a href="http://www.mingw.org/">MinGW</a>. We recommend <a href="http://www.tdragon.net/recentgcc/">TDM's MinGW Build</a>. If using <a href="http://www.mingw.org/">MinGW</a>, you must also have <a href="http://www.mingw.org/wiki/msys">MSYS</a> installed.</p>
 <p>To build Bowtie, extract the sources, change to the extracted directory, and run GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with <a href="http://www.mingw.org/">MinGW</a>, run <code>make</code> from the <a href="http://www.mingw.org/wiki/msys">MSYS</a> command line.</p>
-<p>To support the <a href="#bowtie-options-p"><code>-p</code></a> (multithreading) option, Bowtie needs the <code>pthreads</code> library. To compile Bowtie without <code>pthreads</code> (which disables <a href="#bowtie-options-p"><code>-p</code></a>), use <code>make BOWTIE_PTHREADS=0</code>.</p>
+<p>To support the <a href="#bowtie-options-p"><code>-p</code></a> (multithreading) option, Bowtie needs the <code>pthreads</code> 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.</p>
 <h1 id="the-bowtie-aligner"><a href="#TOC">The <code>bowtie</code> aligner</a></h1>
 <p><code>bowtie</code> 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 <a href="#bowtie-options-v"><code>-v</code></a>/<a href="#bowtie-options-n"><code>-n</code></a>/<a href="#bowtie-options-e"><code>-e</code></a>/<a href="#bowtie-options-l"><code>-l</code></a> options (plus the <a href="#bowtie-options-I"><code>-I</code></a>/<a href="#bowtie-options-X"><code>-X</code></a>/<a href="#bowtie-options-fr"><code>--fr</code></a>/<a href="#bowtie-options-fr"><code>--rf</code></a>/ <a href="#bowtie-options-fr"><code>--ff</code></a> options for paired-end alignment), which define which alignments are legal, and the <a href="#bowtie-options-k"><code>-k</code></a>/<a href="#bowtie-options-a"><code>-a</code></a>/<a href="#bowtie-options-m"><code>-m</code></a>/<a href="#bowtie-options-m"><code>-M</code></a>/<a href="#bowtie-options-best"><code>--best</code></a>/<a href="#bowtie-options-strata"><code>--strata</code></a> options which define which and how many legal alignments should be reported.</p>
 <p>By default, Bowtie enforces an alignment policy similar to <a href="http://maq.sf.net">Maq</a>'s default quality-aware policy (<a href="#bowtie-options-n"><code>-n</code></a> 2 <a href="#bowtie-options-l"><code>-l</code></a> 28 <a href="#bowtie-options-e"><code>-e</code></a> 70). See <a href="#the--n-alignment-mode">the -n alignment mode</a> 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 <a href="#bowtie-options-v"><code>-v</code></a> 2). See <a href="#the--v-alignment-mode">the -v alignment mode</a> section of the manual for details about that mode. <a href="#the--n-alignment-mode">The -n alignment mode</a> and <a href="#the--v-alignment-mode">the -v alignment mode</a> are mutually exclusive.</p>
@@ -1084,12 +1084,6 @@ T2302111203131231130300111123220
 <p>Use <code>&lt;int&gt;</code> as the seed for pseudo-random number generator.</p>
 </td></tr><tr><td>
 
-<pre><code>--cutoff &lt;int&gt;</code></pre>
-</td><td>
-
-<p>Index only the first <code>&lt;int&gt;</code> bases of the reference sequences (cumulative across sequences) and ignore the rest.</p>
-</td></tr><tr><td>
-
 <pre><code>-q/--quiet</code></pre>
 </td><td>