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

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch debian/unstable
in repository sga.

commit 47f18d8232374eb63ca00b0547588b3520f569c7
Author: Afif Elghraoui <afif at debian.org>
Date:   Mon Aug 22 00:18:24 2016 -0700

    Refresh patches
---
 debian/patches/0002-no-rpath.patch                             |  8 ++++----
 debian/patches/0003-do-not-dist-unsup-script.patch             |  4 ++--
 debian/patches/0004-Add-help-to-sga-bam2de.pl.patch            | 10 +++++-----
 debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch |  4 ++--
 debian/patches/0006-remove-google-addsense.patch               |  6 +++---
 5 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/debian/patches/0002-no-rpath.patch b/debian/patches/0002-no-rpath.patch
index e5ca701..3c64791 100644
--- a/debian/patches/0002-no-rpath.patch
+++ b/debian/patches/0002-no-rpath.patch
@@ -3,9 +3,9 @@ From: "Michael R. Crusoe" <michael.crusoe at gmail.com>,
 Date: Wed, 28 May 2014 07:40:21 +0200
 Subject: no-rpath
 
---- a/src/configure.ac
-+++ b/src/configure.ac
-@@ -32,7 +32,7 @@ AC_ARG_WITH(bamtools, AS_HELP_STRING([--
+--- sga.orig/src/configure.ac
++++ sga/src/configure.ac
+@@ -32,7 +32,7 @@
  	[specify directory containing the bamtools library (http://github.com/pezmaster31/bamtools)]))
  
  if test "$with_bamtools" -a -d "$with_bamtools"; then
@@ -14,7 +14,7 @@ Subject: no-rpath
      bamtools_include="-I$with_bamtools/include -I$with_bamtools/include/bamtools"
  fi
  
-@@ -52,7 +52,7 @@ AC_ARG_WITH(hoard, AS_HELP_STRING([--wit
+@@ -52,7 +52,7 @@
  
  # Set library path to user-selected allocator
  if test "$with_hoard" -a -d "$with_hoard"; then
diff --git a/debian/patches/0003-do-not-dist-unsup-script.patch b/debian/patches/0003-do-not-dist-unsup-script.patch
index 71d22ec..31d84f5 100644
--- a/debian/patches/0003-do-not-dist-unsup-script.patch
+++ b/debian/patches/0003-do-not-dist-unsup-script.patch
@@ -6,8 +6,8 @@ Subject: do-not-dist-unsup-script
  src/bin/Makefile.am |    3 +--
  1 file changed, 1 insertion(+), 2 deletions(-)
 
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga.orig/src/bin/Makefile.am
++++ sga/src/bin/Makefile.am
 @@ -1,6 +1,5 @@
  dist_bin_SCRIPTS = \
 -	sga-astat.py \
diff --git a/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch b/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
index b9cfa9f..2569234 100644
--- a/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
+++ b/debian/patches/0004-Add-help-to-sga-bam2de.pl.patch
@@ -6,9 +6,9 @@ Subject: Add --help to sga-bam2de.pl
  src/bin/sga-bam2de.pl |   10 +++++++++-
  1 file changed, 9 insertions(+), 1 deletion(-)
 
---- a/src/bin/sga-bam2de.pl
-+++ b/src/bin/sga-bam2de.pl
-@@ -10,6 +10,7 @@ my $prefix = "";
+--- sga.orig/src/bin/sga-bam2de.pl
++++ sga/src/bin/sga-bam2de.pl
+@@ -10,6 +10,7 @@
  my $numThreads = 1;
  my $mind = -99; # minimum gap size to pass to abyss
  my $mina = 100; # minimum alignment length to pass to abyss
@@ -16,7 +16,7 @@ Subject: Add --help to sga-bam2de.pl
  
  # Filter the abyss distance est histogram to remove insert sizes
  # with fewer than hist_min data points
-@@ -21,7 +22,13 @@ GetOptions("prefix=s" => \$prefix,
+@@ -21,7 +22,13 @@
             "m=i"      => \$minLength,
             "mind=i"   => \$mind,
             "mina=i"   => \$mina,
@@ -31,7 +31,7 @@ Subject: Add --help to sga-bam2de.pl
  
  checkDependency("abyss-fixmate");
  checkDependency("DistanceEst");
-@@ -82,6 +89,7 @@ sub usage
+@@ -82,6 +89,7 @@
      print "                --mind D         Set the minimum distance estimate to test to be D. This should be a negative\n";
      print "                                 number if contigs are expected to overlap. Defaults to -99bp.\n";
      print "                --mina N         Set the minimum alignment length to be N.\n";
diff --git a/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch b/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
index 663488f..e3c5a1e 100644
--- a/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
+++ b/debian/patches/0005-Remove-extensions-on-scripts-we-ship.patch
@@ -6,8 +6,8 @@ Subject: Remove extensions on scripts we ship
  src/bin/Makefile.am |    9 +++++++--
  1 file changed, 7 insertions(+), 2 deletions(-)
 
---- a/src/bin/Makefile.am
-+++ b/src/bin/Makefile.am
+--- sga.orig/src/bin/Makefile.am
++++ sga/src/bin/Makefile.am
 @@ -1,5 +1,10 @@
  dist_bin_SCRIPTS = \
 -	sga-bam2de.pl \
diff --git a/debian/patches/0006-remove-google-addsense.patch b/debian/patches/0006-remove-google-addsense.patch
index f970489..07bdf42 100644
--- a/debian/patches/0006-remove-google-addsense.patch
+++ b/debian/patches/0006-remove-google-addsense.patch
@@ -2,9 +2,9 @@ From: Andreas Tille <tille at debian.org>
 Date: Wed, 28 May 2014 07:40:21 +0200
 Subject: remove Google analytics spying JavaScript
 
---- a/index.html
-+++ b/index.html
-@@ -93,14 +93,5 @@ The package also contains programs to co
+--- sga.orig/index.html
++++ sga/index.html
+@@ -93,14 +93,5 @@
  
    </div>
  

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