debian/mansrc/vmatch.1.adoc

@@ -23,8 +23,8 @@ a combination of options specifying
 * the output mode and output format.
 
 Additionally, if there is more than one algorithm to solve a certain matching
-task, *vmatch* allows to specify which algorithm is to be used. 
-*vmatch* allows to compute the following kinds of matches:
+task, *vmatch* allows one to specify which algorithm is to be used.
+*vmatch* supports computing the following kinds of matches:
 
 . match all substrings of the database sequences against itself. The matches
   can be one of the following kinds:

debian/mansrc/vmatchselect.1.adoc

@@ -36,7 +36,7 @@ options specifying the index and/or the query sequences to be matched, as well
 as options specifying how to match are not available in *vmatchselect*.
 The options of *vmatchselect* have the same meaning as in the program *vmatch*.
 Thus, for a description, see the corresponding documentation. Note that
-*vmatchselect* also allows to use the option "-dbcluster". If *vmatchselect*
+*vmatchselect* also supports the option "-dbcluster". If *vmatchselect*
 is called with this option, then it parses the given match file and performs
 single linkage clustering based on the matches in this file.
 Thus *vmatch* and *vmatchselect* allow to perform hierarchical clustering.
@@ -44,7 +44,7 @@ In a first step an initial set of matches with loose matching criteria is
 computed, using *vmatch*. Then one clusters these matches by calling
 *vmatchselect*. In a second round one applies more strict choices for the
 matches by the using the options "-l", "-leastscore", "-evalue", or
-"-identity", etc. This allows stepwise refinement of clusters without much
+"-identity", etc. This facilitates stepwise refinement of clusters without much
 computational effort and no new index construction for the sequence of a
 cluster. The output of *vmatchselect* is the same as the output of *vmatch*.
 

debian/patches/common-distdir.patch

+Description: Use a common dist directory
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/Makefile
 +++ b/src/Makefile
 @@ -6,9 +6,8 @@

debian/patches/hardening.patch

+Description: Ensure that hardening flags get passed to the compiler calls
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/bin/mkfilegoals.pl
 +++ b/src/bin/mkfilegoals.pl
 @@ -225,7 +225,7 @@

debian/patches/no-symlink.patch

+Description: Do not create symlinks
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/bin/mklink.sh
 +++ b/src/bin/mklink.sh
 @@ -17,7 +17,7 @@

debian/patches/remove-hardcoded-includepaths.patch

+Description: remove hardcoded include paths
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/Makedef-linux-gcc
 +++ b/src/Makedef-linux-gcc
 @@ -15,9 +15,7 @@

debian/patches/skip-doc-installation.patch

+Description: Skip documentation installation (for now).
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/Makefile
 +++ b/src/Makefile
-@@ -187,9 +187,9 @@
+@@ -186,9 +186,9 @@
  	@cp Mkvtree/TRANS/Trans* $(VMATCHDISTDIR)/${SMAPDIR}
  	@cp bin/cleanpp.sh $(VMATCHDISTDIR)
  	@cp bin/Vmatchtrans.pl $(VMATCHDISTDIR)

debian/patches/use-shared-gt-lib.patch

+Description: Use Debian's libgenometools instead of static lib
+ Vmatch was intended to be built as a static binary in a defined build
+ directory with a copy of libgenometools.a in a specific place.
+ In Debian, we have a shared library, so let's use this in the build setup.
+Author: Sascha Steinbiss <satta@debian.org>
+Last-Update: 2020-01-03
 --- a/src/Mkvtree/Makefile
 +++ b/src/Mkvtree/Makefile
 @@ -1,10 +1,10 @@