Sascha Steinbiss pushed to branch master at Debian Med / vmatch
Commits: 4335f0f5 by Sascha Steinbiss at 2020-01-03T10:19:55+01:00 fix spelling in manpages - - - - - b309cc3b by Sascha Steinbiss at 2020-01-03T10:26:59+01:00 add patch headers - - - - - 8 changed files: - debian/mansrc/vmatch.1.adoc - debian/mansrc/vmatchselect.1.adoc - debian/patches/common-distdir.patch - debian/patches/hardening.patch - debian/patches/no-symlink.patch - debian/patches/remove-hardcoded-includepaths.patch - debian/patches/skip-doc-installation.patch - debian/patches/use-shared-gt-lib.patch Changes: ===================================== 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 ===================================== @@ -1,3 +1,6 @@ +Description: Use a common dist directory +Author: Sascha Steinbiss <[email protected]> +Last-Update: 2020-01-03 --- a/src/Makefile +++ b/src/Makefile @@ -6,9 +6,8 @@ ===================================== debian/patches/hardening.patch ===================================== @@ -1,3 +1,6 @@ +Description: Ensure that hardening flags get passed to the compiler calls +Author: Sascha Steinbiss <[email protected]> +Last-Update: 2020-01-03 --- a/src/bin/mkfilegoals.pl +++ b/src/bin/mkfilegoals.pl @@ -225,7 +225,7 @@ ===================================== debian/patches/no-symlink.patch ===================================== @@ -1,3 +1,6 @@ +Description: Do not create symlinks +Author: Sascha Steinbiss <[email protected]> +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 ===================================== @@ -1,3 +1,6 @@ +Description: remove hardcoded include paths +Author: Sascha Steinbiss <[email protected]> +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 ===================================== @@ -1,6 +1,9 @@ +Description: Skip documentation installation (for now). +Author: Sascha Steinbiss <[email protected]> +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 ===================================== @@ -1,3 +1,9 @@ +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 <[email protected]> +Last-Update: 2020-01-03 --- a/src/Mkvtree/Makefile +++ b/src/Mkvtree/Makefile @@ -1,10 +1,10 @@ View it on GitLab: https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6 -- View it on GitLab: https://salsa.debian.org/med-team/vmatch/compare/5fc91a2e3775f1571a8a6e6bf8573dabc98cd666...b309cc3b0ddb156e7a9026ec033d9e1bbe933ee6 You're receiving this email because of your account on salsa.debian.org.
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