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-rw-r--r--sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch48
1 files changed, 0 insertions, 48 deletions
diff --git a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch
deleted file mode 100644
index ff484dfa3ebb..000000000000
--- a/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Author: Andreas Tille <tille@debian.org>
-Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
-Description: Fix spelling
-
---- a/MANUAL
-+++ b/MANUAL
-@@ -544,7 +544,7 @@ The `bowtie`, `bowtie-build` and `bowtie
- actually wrapper scripts that call binary programs as appropriate. The
- wrappers shield users from having to distinguish between "small" and
- "large" index formats, discussed briefly in the following section. The
--appropiate index type is selected based on the input size.
-+appropriate index type is selected based on the input size.
-
- It is recommended that you always run the bowtie wrappers and not run
- the binaries directly.
---- a/MANUAL.markdown
-+++ b/MANUAL.markdown
-@@ -559,7 +559,7 @@ The `bowtie`, `bowtie-build` and `bowtie
- actually wrapper scripts that call binary programs as appropriate. The
- wrappers shield users from having to distinguish between "small" and
- "large" index formats, discussed briefly in the following section. The
--appropiate index type is selected based on the input size.
-+appropriate index type is selected based on the input size.
-
- It is recommended that you always run the bowtie wrappers and not run
- the binaries directly.
---- a/doc/manual.html
-+++ b/doc/manual.html
-@@ -201,7 +201,7 @@ T2302111203131231130300111123220
- <p>Like other platforms, SOLiD supports generation of paired-end reads. When colorspace alignment is enabled, the default paired-end orientation setting is <a href="#bowtie-options-fr"><code>--ff</code></a>. This is because most SOLiD datasets have that orientation.</p>
- <p>Note that SOLiD-generated read files can have &quot;orphaned&quot; mates; i.e. mates without a correpsondingly-named mate in the other file. To avoid problems due to orphaned mates, SOLiD paired-end output should first be converted to <code>.csfastq</code> files with unpaired mates omitted. This can be accomplished using, for example, [Galaxy]'s conversion tool (click &quot;NGS: QC and manipulation&quot;, then &quot;SOLiD-to-FASTQ&quot; in the left-hand sidebar).</p>
- <h2 id="wrapper-scripts">Wrapper scripts</h2>
--<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropiate index type is selected based on the input size.</p>
-+<p>The <code>bowtie</code>, <code>bowtie-build</code> and <code>bowtie-inspect</code> executables are actually wrapper scripts that call binary programs as appropriate. The wrappers shield users from having to distinguish between &quot;small&quot; and &quot;large&quot; index formats, discussed briefly in the following section. The appropriate index type is selected based on the input size.</p>
- <p>It is recommended that you always run the bowtie wrappers and not run the binaries directly.</p>
- <h2 id="small-and-large-indexes">Small and large indexes</h2>
- <p><code>bowtie-build</code> can index reference genomes of any size. For genomes less than about 4 billion nucleotides in length, <code>bowtie-build</code> builds a &quot;small&quot; index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a &quot;large&quot; index using 64-bit numbers. Small indexes are stored in files with the <code>.ebwt</code> extension, and large indexes are stored in files with the <code>.ebwtl</code> extension. The user need not worry about whether a particular index is small or large; the wrapper scripts will automatically build and use the appropriate index.</p>
---- a/ref_read.cpp
-+++ b/ref_read.cpp
-@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in,
- << "reference into smaller chunks and index each independently." << endl;
- #else
- cerr << "Error: Reference sequence has more than 2^32-1 characters! Please try to" << endl
-- << "build a large index instead using the appropiate options." << endl;
-+ << "build a large index instead using the appropriate options." << endl;
- #endif
- throw 1;
- }