[med-svn] [genometools] 01/02: update spelling patch

[Sascha Steinbiss]

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sascha-guest pushed a commit to branch master
in repository genometools.

commit f5192cfd644f6e5ef8f6e208c9b79886aa0758d6
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Tue Mar 15 21:06:44 2016 +0000

    update spelling patch
---
 debian/patches/spelling | 55 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)

diff --git a/debian/patches/spelling b/debian/patches/spelling
index 33fe28d..6899c41 100644
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -239,3 +239,58 @@ Last-Update: 2016-03-07
  <div class="literalblock">
  <div class="content">
  <pre><tt>gt suffixerator -protein -ssp -tis -des -sds -kys -indexname fastaindex \
+--- a/src/extended/affinealign.h
++++ b/src/extended/affinealign.h
+@@ -52,7 +52,7 @@
+ 
+ /* Computes a global alignment with affine gapcosts in square space. Use of this
+    function requires an initialised <scorehandler> with cost values an
+-   initalised <spacemanager>, the target alignment <align> and input sequences
++   initialised <spacemanager>, the target alignment <align> and input sequences
+    <useq> and <vseq> and lengths <ulen> and <vlen>. Returns affine cost
+    value of global alignment. */
+ GtWord gt_affinealign_with_Management(GtLinspaceManagement *spacemanager,
+--- a/src/extended/type_node.c
++++ b/src/extended/type_node.c
+@@ -109,7 +109,7 @@
+ 
+    That is, if X is_a Y and Z part_of Y, then Z part_of X.
+ 
+-   The method maintains a <node_stack> containing the inital <node> and all
++   The method maintains a <node_stack> containing the initial <node> and all
+    its 'is_a' children.
+ 
+    Example from Sequence Ontology (we are looking at mRNA and exon, see
+--- a/src/gth/align_protein.c
++++ b/src/gth/align_protein.c
+@@ -188,7 +188,7 @@
+   return retracenames[retrace];
+ }
+ 
+-/* the following function initalizes the input structure */
++/* the following function initializes the input structure */
+ static void initinput(GthAlignInputProtein *input,
+                       const unsigned char *ref_seq_orig,
+                       GthInput *gth_input)
+--- a/src/tools/gt_condenseq_compress.c
++++ b/src/tools/gt_condenseq_compress.c
+@@ -108,7 +108,7 @@
+ 
+   /* -initsize */
+   option = gt_option_new_uword("initsize",
+-                               "length of inital unique database in bases, "
++                               "length of initial unique database in bases, "
+                                "should be larger than -alignlength",
+                                &arguments->initsize, GT_UNDEF_UWORD);
+   gt_option_parser_add_option(op, option);
+--- a/src/tools/gt_linspace_align.c
++++ b/src/tools/gt_linspace_align.c
+@@ -186,7 +186,7 @@
+   optionshowscore = gt_option_new_bool("showscore", "show score for alignment, "
+                                        "please note it will calculate costs "
+                                        "for global alignments and scores for "
+-                                       "local alignemnts always, independtly "
++                                       "local alignments always, independently "
+                                        "of input ",
+                                        &arguments->showscore, false);
+   gt_option_parser_add_option(op, optionshowscore);

-- 
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