[med-svn] [canu] 03/04: Refresh patches

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository canu.

commit e9a8c24a67cdf0b70dd0ed638d07f30b813fb0de
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Mar 20 22:47:18 2017 -0400

    Refresh patches
---
 debian/patches/external-deps.patch              |  2 +-
 debian/patches/use-debian-mhap-at-runtime.patch | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/debian/patches/external-deps.patch b/debian/patches/external-deps.patch
index 7965606..516daf8 100644
--- a/debian/patches/external-deps.patch
+++ b/debian/patches/external-deps.patch
@@ -3,7 +3,7 @@ Author: Afif Elghraoui <afif at debian.org>
 Forwarded: not-needed
 --- canu.orig/src/main.mk
 +++ canu/src/main.mk
-@@ -145,7 +145,6 @@
+@@ -157,7 +157,6 @@
                  \
                  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 108e459..f71079a 100644
--- a/debian/patches/use-debian-mhap-at-runtime.patch
+++ b/debian/patches/use-debian-mhap-at-runtime.patch
@@ -4,21 +4,21 @@ Forwarded: not-needed
 Last-Update: 2016-03-20
 --- canu.orig/src/pipelines/canu/OverlapMhap.pm
 +++ canu/src/pipelines/canu/OverlapMhap.pm
-@@ -357,7 +357,7 @@
+@@ -350,7 +350,7 @@
      print F "cd $path/blocks\n";
      print F "\n";
-     print F "$javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n";
+     print F "$javaPath -d64 -server -Xmx", $javaMemory, "m \\\n";
 -    print F "  -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n";
 +    print F "  -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java/mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n";
-     print F "  --repeat-weight 0.9 -k $merSize \\\n";
+     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("${tag}MhapNoTf") == 1);
-@@ -434,7 +434,7 @@
+@@ -421,7 +421,7 @@
      print F "\n";
      print F "if [ ! -e \"$path/results/\$qry.mhap\" ] ; then\n";
-     print F "  $javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n";
+     print F "  $javaPath -d64 -server -Xmx", $javaMemory, "m \\\n";
 -    print F "    -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "\$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n";
 +    print F "    -jar " . ($^O eq "cygwin" ? "\$(cygpath -w " : "") . "/usr/share/java//mhap.jar " . ($^O eq "cygwin" ? ")" : "") . "\\\n";
-     print F "    --repeat-weight 0.9 -k $merSize \\\n";
+     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);

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