Package: bowtie / 1.2.2+dfsg-4

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Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
Description: Fix spelling

--- bowtie.orig/MANUAL
+++ bowtie/MANUAL
@@ -543,7 +543,7 @@
 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.
--- bowtie.orig/MANUAL.markdown
+++ bowtie/MANUAL.markdown
@@ -558,7 +558,7 @@
 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.
--- bowtie.orig/doc/manual.html
+++ bowtie/doc/manual.html
@@ -199,7 +199,7 @@
 <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>
--- bowtie.orig/ref_read.cpp
+++ bowtie/ref_read.cpp
@@ -263,7 +263,7 @@
 				     << "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;
 			}
--- bowtie.orig/shmem.h
+++ bowtie/shmem.h
@@ -67,7 +67,7 @@
 				cerr << "EEXIST" << endl;
 			} else if(errno == EINVAL) {
 				cerr << "Warning: shared-memory chunk's segment size doesn't match expected size (" << (shmemLen) << ")" << endl
-					 << "Deleteing old shared memory block and trying again." << endl;
+					 << "Deleting old shared memory block and trying again." << endl;
 				shmid = shmget(key, 0, 0);
 				if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
 					cerr << "shmctl returned " << ret
@@ -105,7 +105,7 @@
 		if(ds.shm_segsz != shmemLen) {
 			cerr << "Warning: shared-memory chunk's segment size (" << ds.shm_segsz
 				 << ") doesn't match expected size (" << shmemLen << ")" << endl
-				 << "Deleteing old shared memory block and trying again." << endl;
+				 << "Deleting old shared memory block and trying again." << endl;
 			if((ret = shmctl(shmid, IPC_RMID, &ds)) < 0) {
 				cerr << "shmctl returned " << ret << " for IPC_RMID and errno is " << errno << endl;
 				throw 1;