[med-svn] [canu] 05/06: Update patch

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository canu.

commit 6a76a517bb1b3d724b2b7420a01e2afbb1ee6b77
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Wed Jul 13 08:47:51 2016 -0700

    Update patch
---
 debian/patches/use-debian-mhap-at-runtime.patch | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/debian/patches/use-debian-mhap-at-runtime.patch b/debian/patches/use-debian-mhap-at-runtime.patch
index 04ef063..108e459 100644
--- a/debian/patches/use-debian-mhap-at-runtime.patch
+++ b/debian/patches/use-debian-mhap-at-runtime.patch
@@ -4,12 +4,21 @@ Forwarded: not-needed
 Last-Update: 2016-03-20
 --- canu.orig/src/pipelines/canu/OverlapMhap.pm
 +++ canu/src/pipelines/canu/OverlapMhap.pm
-@@ -367,7 +367,7 @@
+@@ -357,7 +357,7 @@
      print F "cd $path/blocks\n";
      print F "\n";
-     print F "$javaPath -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n";
--    print F "  -jar \$bin/mhap-" . getGlobal("${tag}MhapVersion") . ".jar \\\n";
-+    print F "  -jar /usr/share/java/mhap-*.jar \\\n";
-     print F "  --weighted -k $merSize \\\n";
-     print F "  --num-hashes $numHashes \\\n";
-     print F "  --num-min-matches $minNumMatches \\\n";
+     print F "$javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n";
+-    print F "  -jar " . ($^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 $merSize \\\n";
+     print F "  --supress-noise 2 \\\n"  if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
+     print F "  --no-tf \\\n"            if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);
+@@ -434,7 +434,7 @@
+     print F "\n";
+     print F "if [ ! -e \"$path/results/\$qry.mhap\" ] ; then\n";
+     print F "  $javaPath -d64 -server -Xmx", getGlobal("${tag}mhapMemory"), "g \\\n";
+-    print F "    -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 $merSize \\\n";
+     print F "    --supress-noise 2 \\\n"  if (defined(getGlobal("${tag}MhapFilterUnique")) && getGlobal("${tag}MhapFilterUnique") == 1);
+     print F "    --no-tf \\\n"            if (defined(getGlobal("${tag}MhapNoTf")) && getGlobal("${tag}MhapNoTf") == 1);

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