[med-svn] [bowtie] 04/09: Update spelling.patch

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository bowtie.

commit e77c58a4a5fc169b7a746a083a92b60fb789ded7
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Oct 19 17:03:43 2017 +0200

    Update spelling.patch
---
 debian/patches/spelling.patch | 44 +++++++++++++++++++++++++++++++------------
 1 file changed, 32 insertions(+), 12 deletions(-)

diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index eb644c3..6d18f1f 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -2,9 +2,9 @@ Author: Andreas Tille <tille at debian.org>
 Last-Update: Thu, 01 Oct 2015 09:47:23 +0200
 Description: Fix spelling
 
---- a/MANUAL
-+++ b/MANUAL
-@@ -543,7 +543,7 @@ The `bowtie`, `bowtie-build` and `bowtie
+--- 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
@@ -13,9 +13,9 @@ Description: Fix spelling
  
  It is recommended that you always run the bowtie wrappers and not run
  the binaries directly.
---- a/MANUAL.markdown
-+++ b/MANUAL.markdown
-@@ -558,7 +558,7 @@ The `bowtie`, `bowtie-build` and `bowtie
+--- 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
@@ -24,9 +24,9 @@ Description: Fix spelling
  
  It is recommended that you always run the bowtie wrappers and not run
  the binaries directly.
---- a/doc/manual.html
-+++ b/doc/manual.html
-@@ -199,7 +199,7 @@ T2302111203131231130300111123220
+--- 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 "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>
@@ -35,9 +35,9 @@ Description: Fix spelling
  <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> e [...]
---- a/ref_read.cpp
-+++ b/ref_read.cpp
-@@ -263,7 +263,7 @@ fastaRefReadSizes(vector<FileBuf*>& in,
+--- 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
@@ -46,3 +46,23 @@ Description: Fix spelling
  #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;

-- 
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