Strip extraneous whitespace (#1390)

dib-lab · Jun 23, 2016 · 8300de0 · 8300de0
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diff --git a/CITATION b/CITATION
@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 .. If you update this file then you may need to update the citations in

diff --git a/doc/contributors.rst b/doc/contributors.rst
@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 *********************************
@@ -58,7 +58,7 @@ Adina Howe, Rosangela Canino-Koning, and Arend Hintze contributed
 significantly to discussions of approaches and algorithms; Adina wrote
 a number of scripts.
 
-Jared T. Simpson (University of Cambridge, Sanger Institute) contributed 
+Jared T. Simpson (University of Cambridge, Sanger Institute) contributed
 paired-end support for digital normalization.
 
 Eric McDonald thoroughly revised many aspects of the code base, made

diff --git a/doc/index.rst b/doc/index.rst
@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 ###################################################################
@@ -113,12 +113,12 @@ Details
 There are two mailing lists dedicated to khmer, an announcements-only list and
 a discussion list. To search their archives and sign-up for them, please visit
 the following URLs:
-    
+
     * Discussion: http://lists.idyll.org/listinfo/khmer
 
     * Announcements: http://lists.idyll.org/listinfo/khmer-announce
 
-The archives for the khmer mailing list are available at: 
+The archives for the khmer mailing list are available at:
 http://lists.idyll.org/pipermail/khmer/
 
 khmer development was initially supported by AFRI Competitive Grant

diff --git a/doc/introduction.rst b/doc/introduction.rst
@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 *********************
@@ -43,46 +43,46 @@ Introduction to khmer
 Introduction
 ============
 
-khmer is a library and toolkit for doing k-mer-based dataset analysis and 
-transformations.  Our focus in developing it has been on scaling assembly of 
+khmer is a library and toolkit for doing k-mer-based dataset analysis and
+transformations.  Our focus in developing it has been on scaling assembly of
 metagenomes and mRNA.
 
-khmer can be used for a number of transformations, including inexact 
-transformations (abundance filtering and error trimming) and exact 
-transformations (graph-size filtering, to throw away disconnected reads; and 
-partitioning, to split reads into disjoint sets).  Of these, only partitioning 
-is not constant memory.  In all cases, the memory required for assembly with 
-Velvet or another de Bruijn graph assembler will be more than the memory 
-required to use our software. Our software will not increase the memory required 
-for Velvet, either, although we may not be able to *decrease* the memory 
+khmer can be used for a number of transformations, including inexact
+transformations (abundance filtering and error trimming) and exact
+transformations (graph-size filtering, to throw away disconnected reads; and
+partitioning, to split reads into disjoint sets).  Of these, only partitioning
+is not constant memory.  In all cases, the memory required for assembly with
+Velvet or another de Bruijn graph assembler will be more than the memory
+required to use our software. Our software will not increase the memory required
+for Velvet, either, although we may not be able to *decrease* the memory
 required for assembly for every data set.
 
-Most of khmer relies on an underlying probabilistic data structure known as a 
-`Bloom filter <http://en.wikipedia.org/wiki/Bloom_filter>`__ (also see 
-`Count-Min Sketch <http://dimacs.rutgers.edu/~graham/pubs/papers/cm-full.pdf>`__ 
-and `These Are Not The k-mers You're Looking For 
-<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111482/>`__), which is essentially 
-a set of hash tables, each of different size, with no collision detection. These 
-hash tables are used to store the presence of specific k-mers and/or their 
-count.  The lack of collision detection means that the Bloom filter may report a 
-k-mer as being "present" when it is not, in fact, in the data set; however, it 
-will never incorrectly report a k-mer as being absent when it *is* present.  
-This one-sided error makes the Bloom filter very useful for certain kinds of 
+Most of khmer relies on an underlying probabilistic data structure known as a
+`Bloom filter <http://en.wikipedia.org/wiki/Bloom_filter>`__ (also see
+`Count-Min Sketch <http://dimacs.rutgers.edu/~graham/pubs/papers/cm-full.pdf>`__
+and `These Are Not The k-mers You're Looking For
+<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111482/>`__), which is essentially
+a set of hash tables, each of different size, with no collision detection. These
+hash tables are used to store the presence of specific k-mers and/or their
+count.  The lack of collision detection means that the Bloom filter may report a
+k-mer as being "present" when it is not, in fact, in the data set; however, it
+will never incorrectly report a k-mer as being absent when it *is* present.
+This one-sided error makes the Bloom filter very useful for certain kinds of
 operations.
 
-khmer is also independent of a specific k-size (K), and currently works for 
+khmer is also independent of a specific k-size (K), and currently works for
 K <= 32.  We will be integrating code for K<=64 soon.
 
-khmer is implemented in C++ with a Python wrapper, which is what all of the 
+khmer is implemented in C++ with a Python wrapper, which is what all of the
 scripts use.
 
-Documentation for khmer is provided on the Web sites for 
-`khmer-protocols <http://khmer-protocols.readthedocs.org>`__ and `khmer-recipes 
-<http://khmer-recipes.readthedocs.org>`__. khmer-protocols provides detailed 
-protocols for using khmer to analyze either a transcriptome or a metagenome. 
-khmer-recipes provides individual recipes for using khmer in a variety of 
-sequence-oriented tasks such as extracting reads by coverage, estimating a 
-genome or metagenome size from unassembled reads, and error-trimming reads via 
+Documentation for khmer is provided on the Web sites for
+`khmer-protocols <http://khmer-protocols.readthedocs.org>`__ and `khmer-recipes
+<http://khmer-recipes.readthedocs.org>`__. khmer-protocols provides detailed
+protocols for using khmer to analyze either a transcriptome or a metagenome.
+khmer-recipes provides individual recipes for using khmer in a variety of
+sequence-oriented tasks such as extracting reads by coverage, estimating a
+genome or metagenome size from unassembled reads, and error-trimming reads via
 streaming k-mer abundance.
 
 Using khmer
@@ -114,16 +114,16 @@ and a few other random functions.
 Practical considerations
 ========================
 
-The most important thing to think about when using khmer is whether or not the 
-transformation or filter you're applying is appropriate for the data you're 
-trying to assemble.  Two of the most powerful operations available in khmer, 
-graph-size filtering and graph partitioning, only make sense for assembly 
-datasets with many theoretically unconnected components.  This is typical of 
+The most important thing to think about when using khmer is whether or not the
+transformation or filter you're applying is appropriate for the data you're
+trying to assemble.  Two of the most powerful operations available in khmer,
+graph-size filtering and graph partitioning, only make sense for assembly
+datasets with many theoretically unconnected components.  This is typical of
 metagenomic data sets.
 
-The second most important consideration is memory usage.  The effectiveness of 
-all of the Bloom filter-based functions (which is everything interesting in 
-khmer!) depends critically on having enough memory to do a good job.  See 
+The second most important consideration is memory usage.  The effectiveness of
+all of the Bloom filter-based functions (which is everything interesting in
+khmer!) depends critically on having enough memory to do a good job.  See
 :doc:`user/choosing-table-sizes` for more information.
 
 Copyright and license
@@ -132,5 +132,5 @@ Copyright and license
 Portions of khmer are Copyright California Institute of Technology,
 where the exact counting code was first developed. All other code developed
 through 2014 is copyright Michigan State University. Portions are copyright
-Michigan State University and Regents of the University of California.  
+Michigan State University and Regents of the University of California.
 All the code is freely available for use and re-use under the BSD License.
diff --git a/doc/roadmap.rst b/doc/roadmap.rst
@@ -4,24 +4,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -33,7 +33,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 ***************************

diff --git a/doc/whats-new-2.0.rst b/doc/whats-new-2.0.rst
@@ -3,24 +3,24 @@
    Copyright (C) 2015 The Regents of the University of California.
    It is licensed under the three-clause BSD license; see LICENSE.
    Contact: khmer-project@idyll.org
-   
+
    Redistribution and use in source and binary forms, with or without
    modification, are permitted provided that the following conditions are
    met:
-   
+
     * Redistributions of source code must retain the above copyright
       notice, this list of conditions and the following disclaimer.
-   
+
     * Redistributions in binary form must reproduce the above
       copyright notice, this list of conditions and the following
       disclaimer in the documentation and/or other materials provided
       with the distribution.
-   
+
     * Neither the name of the Michigan State University nor the names
       of its contributors may be used to endorse or promote products
       derived from this software without specific prior written
       permission.
-   
+
    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
@@ -32,7 +32,7 @@
    THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
    (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-   
+
    Contact: khmer-project@idyll.org
 
 ************************