[med-svn] [canu] 02/05: New upstream version

[Andreas Tille]

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tille pushed a commit to branch master
in repository canu.

commit 63c8db01404c1ba3f079a7ccfbf3174c8d0ae6c6
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 2 15:31:05 2017 +0200

    New upstream version
---
 debian/changelog                                | 7 +++++++
 debian/patches/external-deps.patch              | 6 +++---
 debian/patches/use-debian-mhap-at-runtime.patch | 8 ++++----
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c4e273b..08b5f27 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+canu (1.6+dfsg-1) UNRELEASED; urgency=medium
+
+  * Team upload
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Sat, 02 Sep 2017 15:30:21 +0200
+
 canu (1.5+dfsg-1) unstable; urgency=medium
 
   * New upstream release
diff --git a/debian/patches/external-deps.patch b/debian/patches/external-deps.patch
index 9f82882..d3f6e03 100644
--- a/debian/patches/external-deps.patch
+++ b/debian/patches/external-deps.patch
@@ -1,9 +1,9 @@
 Description: Use Debian-packaged MHAP
 Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
---- canu.orig/src/main.mk
-+++ canu/src/main.mk
-@@ -194,7 +194,6 @@
+--- a/src/main.mk
++++ b/src/main.mk
+@@ -193,7 +193,6 @@ SUBMAKEFILES := stores/gatekeeperCreate.
                  \
                  overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.mk \
                  \
diff --git a/debian/patches/use-debian-mhap-at-runtime.patch b/debian/patches/use-debian-mhap-at-runtime.patch
index f96d1e2..3c6edab 100644
--- a/debian/patches/use-debian-mhap-at-runtime.patch
+++ b/debian/patches/use-debian-mhap-at-runtime.patch
@@ -2,9 +2,9 @@ Description: Use mhap jar from /usr/share/java
 Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
 Last-Update: 2016-03-20
---- canu.orig/src/pipelines/canu/OverlapMhap.pm
-+++ canu/src/pipelines/canu/OverlapMhap.pm
-@@ -378,7 +378,7 @@
+--- a/src/pipelines/canu/OverlapMhap.pm
++++ b/src/pipelines/canu/OverlapMhap.pm
+@@ -378,7 +378,7 @@ sub mhapConfigure ($$$) {
      print F "cd ./blocks\n";
      print F "\n";
      print F "$javaPath -d64 -server -Xmx", $javaMemory, "m \\\n";
@@ -13,7 +13,7 @@ Last-Update: 2016-03-20
      print F "  --repeat-weight 0.9 --repeat-idf-scale 10 -k $merSize \\\n";
      print F "  --supress-noise 2 \\\n"  if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
      print F "  --no-tf \\\n"            if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
-@@ -477,7 +477,7 @@
+@@ -478,7 +478,7 @@ sub mhapConfigure ($$$) {
      print F "\n";
      print F "if [ ! -e ./results/\$qry.mhap ] ; then\n";
      print F "  $javaPath -d64 -server -Xmx", $javaMemory, "m \\\n";

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