[med-svn] [bedtools] 04/10: Delete reference to removed image from Debian shipped doc

[Andreas Tille]

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tille pushed a commit to branch master
in repository bedtools.

commit 380ad92a35f8ba62740338aad93db3f350fa7e43
Author: Andreas Tille <tille at debian.org>
Date:   Mon Jul 18 16:15:09 2016 +0200

    Delete reference to removed image from Debian shipped doc
---
 debian/changelog                                    |  1 +
 debian/patches/fix_test_script.patch                |  2 +-
 debian/patches/remove_barski_binding_site.png.patch | 20 ++++++++++++++++++++
 debian/patches/series                               |  1 +
 4 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/debian/changelog b/debian/changelog
index 23d14ec..5b3f9ee 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -10,6 +10,7 @@ bedtools (2.26.0+dfsg-1) UNRELEASED; urgency=medium
   * Remove docs/content/images/tool-glyphs/barski_binding_site.png from upstream
     tarball since it is from
     Jothi et al, 2008, doi:10.1093/nar/gkn488, licensed under no-DFSG CC-BY-NC 2.0
+  * Delete reference to removed image from Debian shipped doc
 
  -- Charles Plessy <plessy at debian.org>  Thu, 07 Jul 2016 13:58:08 +0900
 
diff --git a/debian/patches/fix_test_script.patch b/debian/patches/fix_test_script.patch
index 6c3e902..79bd5e9 100644
--- a/debian/patches/fix_test_script.patch
+++ b/debian/patches/fix_test_script.patch
@@ -4,7 +4,7 @@ Description: Use environment variable to find bedtools in all cases
 
 --- a/test/merge/test-merge.sh
 +++ b/test/merge/test-merge.sh
-@@ -444,7 +444,7 @@ chr1	30	100	.,.,.
+@@ -445,7 +445,7 @@ chr1	30	100	.,.,.
  chr2	10	20	.
  chr2	30	40	.
  chr2	42	100	.,." >exp
diff --git a/debian/patches/remove_barski_binding_site.png.patch b/debian/patches/remove_barski_binding_site.png.patch
new file mode 100644
index 0000000..0ef84ee
--- /dev/null
+++ b/debian/patches/remove_barski_binding_site.png.patch
@@ -0,0 +1,20 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 18 Jul 2016 16:13:29 +0200
+Desctiption: Delete reference to removed file
+
+--- a/docs/content/tools/genomecov.rst
++++ b/docs/content/tools/genomecov.rst
+@@ -346,11 +346,8 @@ overlaps to be performed.
+ Coverage by fragment
+ ==============================================================================
+ 
+-|
+-
+-.. image:: ../images/tool-glyphs/barski_binding_site.png
+-
+-|
++For the Debian package the image barski_binding_site.png from Jothi et al, 2008, doi:10.1093/nar/gkn488
++was removed from this doc since it is licensed under no-DFSG CC-BY-NC 2.0 and thus not distributable.
+ 
+ In ChiP-Seq the binding site is usually not at the coordinate where reads map,
+ but in the middle of the fragment. For this reason we often try to estimate average fragment size
diff --git a/debian/patches/series b/debian/patches/series
index aeb5e3a..78ea556 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 gzstream.h.patch
 fix_test_script.patch
+remove_barski_binding_site.png.patch

-- 
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