[med-svn] [snap-aligner] 01/01: secure Vcs-Browser & fix spelling error

[Michael Crusoe]

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

commit 752dddfe184b16ac59a9bb41312b74adfe2248f6
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date:   Wed Feb 24 07:40:05 2016 -0800

    secure Vcs-Browser & fix spelling error
---
 debian/changelog                    | 2 +-
 debian/control                      | 2 +-
 debian/patches/non-x86-and-kfreebsd | 2 +-
 debian/patches/spelling             | 9 +++++++++
 4 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index e1a4464..7c743c1 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,7 +2,7 @@ snap-aligner (0.18~1.0~beta.18+dfsg1-3) UNRELEASED; urgency=medium
 
   * Add support for kfreebsd and non-x86, thanks to Aaron M. Ucko
     <ucko at debian.org> (Closes: #812551, #812550)
-  * Drop attempt at 32-bit compatability, as per upstream we need >4GB memory
+  * Drop attempt at 32-bit compatibility, as per upstream we need >4GB memory
     space for real uses of this tool.
 
  -- Michael R. Crusoe <crusoe at ucdavis.edu>  Mon, 25 Jan 2016 00:06:51 -0800
diff --git a/debian/control b/debian/control
index abb33fa..09692f0 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 9),
                help2man,
                zlib1g-dev
 Standards-Version: 3.9.7
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/snap-aligner.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snap-aligner.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/snap-aligner.git
 Homepage: http://snap.cs.berkeley.edu/
 
diff --git a/debian/patches/non-x86-and-kfreebsd b/debian/patches/non-x86-and-kfreebsd
index 5c7f6c6..649d296 100644
--- a/debian/patches/non-x86-and-kfreebsd
+++ b/debian/patches/non-x86-and-kfreebsd
@@ -1,4 +1,4 @@
-Description: Uses more liberal CPP defines to add compatability to kfreebsd &
+Description: Uses more liberal CPP defines to add compatibility to kfreebsd &
 non-x86 systems
 Author: Michael R. Crusoe <crusoe at ucdavis.edu> and Aaron M. Ucko <ucko at debian.org>
 --- snap-aligner.orig/SNAPLib/Compat.cpp
diff --git a/debian/patches/spelling b/debian/patches/spelling
index 9b24014..5720bf5 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -3,6 +3,15 @@ Description: typo fix
 Forwarded: https://github.com/amplab/snap/pull/66
 --- snap-aligner.orig/SNAPLib/AlignerOptions.cpp
 +++ snap-aligner/SNAPLib/AlignerOptions.cpp
+@@ -145,7 +145,7 @@
+         "  -R   Specify the entire read group line for the SAM/BAM output.  This must include an ID tag.  If it doesn't start with\n"
+         "       '@RG' SNAP will add that.  Specify tabs by \\t.  Two backslashes will generate a single backslash.\n"
+         "       backslash followed by anything else is illegal.  So, '-R @RG\\tID:foo\\tDS:my data' would generate reads\n"
+-        "       with defualt tag foo, and an @RG line that also included the DS:my data field.\n"
++        "       with default tag foo, and an @RG line that also included the DS:my data field.\n"
+         "  -sa  Include reads from SAM or BAM files with the secondary (0x100) or supplementary (0x800) flag set; default is to drop them.\n"
+         "  -om  Output multiple alignments.  Takes as a parameter the maximum extra edit distance relative to the best alignment\n"
+         "       to allow for secondary alignments\n"
 @@ -173,7 +173,7 @@
          "  -dp  Edit distance as a percentage of read length (single only, overrides -d)\n"
  #endif

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