[med-svn] [snap-aligner] 01/01: add missing file copyright & squash another typo

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository snap-aligner.

commit 8ad3f161b8128d6399177f8d99810ffc2d3b25f7
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Wed Jan 20 08:41:00 2016 -0800

    add missing file copyright & squash another typo
---
 debian/copyright        | 3 ++-
 debian/patches/spelling | 9 +++++++++
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/debian/copyright b/debian/copyright
index 3890a73..068483a 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -14,7 +14,8 @@ Files: debian/*
 Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
 License: Apache-2.0
 
-Files: import/pdclibhdfs/inc/native_mini_dfs.h 
+Files: import/pdclibhdfs/inc/native_mini_dfs.h
+ import/pdclibhdfs/inc/stdint.h-xx
 Copyright: (c) 2006-2013 Alexander Chemeris
 License: BSD-3-clause
 
diff --git a/debian/patches/spelling b/debian/patches/spelling
index b27c719..6c06842 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -2,6 +2,15 @@ Author: Michael R. Crusoe
 Description: typo fix
 --- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
 +++ snap-aligner/SNAPLib/AlignerOptions.cpp
+@@ -173,7 +173,7 @@
+         "  -dp  Edit distance as a percentage of read length (single only, overrides -d)\n"
+ #endif
+ 		"  -nu  No Ukkonen: don't reduce edit distance search based on prior candidates. This option is purely for\n"
+-		"       evalutating the performance effect of using Ukkonen's algorithm rather than Smith-Waterman, and specifying\n"
++		"       evaluating the performance effect of using Ukkonen's algorithm rather than Smith-Waterman, and specifying\n"
+ 		"       it will slow down execution without improving the alignments.\n"
+ 		"  -no  No Ordering: don't order the evalutation of reads so as to select more likely candidates first.  This option\n"
+ 		"       is purely for evaluating the performance effect of the read evaluation order, and specifying it will slow\n"
 @@ -208,7 +208,7 @@
  
      WriteErrorMessage("When specifying an input or output file, you can simply list the filename, in which case\n"

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