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Diffstat (limited to 'sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch')
| -rw-r--r-- | sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch | 48 |
1 files changed, 48 insertions, 0 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 new file mode 100644 index 000000000000..ff484dfa3ebb --- /dev/null +++ b/sci-biology/bowtie/files/bowtie-1.1.2-spelling.patch @@ -0,0 +1,48 @@ +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 "orphaned" 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 "NGS: QC and manipulation", then "SOLiD-to-FASTQ" 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 "small" and "large" 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 "small" and "large" 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 "small" index using 32-bit numbers in various parts of the index. When the genome is longer, <code>bowtie-build</code> builds a "large" 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; + } |