Merge commit 'upstream/0.2.5'

diff --git a/debian/changelog b/debian/changelog
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--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,13 @@
+tabix (0.2.4-1) unstable; urgency=low
+
+  * New upstream release.
+  * Incremented Standards-Version to reflect conformance with Policy 3.9.2
+    (debian/control).
+
+ -- Charles Plessy <plessy@debian.org>  Tue, 12 Apr 2011 17:15:33 +0900
+
+tabix (0.2.3-1) unstable; urgency=low
+
+  * Initial release (Closes: #606446)
+
+ -- Charles Plessy <plessy@debian.org>  Wed, 19 Jan 2011 22:16:39 +0900

diff --git a/debian/compat b/debian/compat
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+++ b/debian/compat
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+8

diff --git a/debian/control b/debian/control
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+++ b/debian/control
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+Source: tabix
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy@debian.org>
+Build-Depends: cdbs, debhelper (>= 8), zlib1g-dev
+Standards-Version: 3.9.2
+Homepage: http://samtools.sourceforge.net/tabix.shtml
+Vcs-Git: git://git.debian.org/debian-med/tabix.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/tabix.git
+
+Package: tabix
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: generic indexer for TAB-delimited genome position files
+ Tabix indexes files where some columns indicate sequence coordinates: name
+ (usually a chromosme), start and stop. The input data file must be position
+ sorted and compressed by bgzip (provided in this package), which has a gzip
+ like interface. After indexing, tabix is able to quickly retrieve data lines by
+ chromosomal coordinates. Fast data retrieval also works over network if an URI
+ is given as a file name.

diff --git a/debian/copyright b/debian/copyright
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+++ b/debian/copyright
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+Format: http://dep.debian.net/deps/dep5/
+Source: http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.4.tar.bz2
+
+Files: *
+Copyright: © 2008 Genome Research Ltd (GRL).
+ © 2008 Broad Institute / Massachusetts Institute of Technology
+ © 2009 Genome Research Ltd (GRL), 2010 Broad Institute
+ © 2010 Broad Institute.
+License: MIT
+
+Files: python/*
+Copyright: © 2011 Seoul National University.
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files (the
+ "Software"), to deal in the Software without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Software, and to
+ permit persons to whom the Software is furnished to do so, subject to
+ the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ SOFTWARE.

diff --git a/debian/docs b/debian/docs
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+++ b/debian/docs
@@ -0,0 +1 @@
+NEWS

diff --git a/debian/examples b/debian/examples
new file mode 100644 (file)
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--- /dev/null
+++ b/debian/examples
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+example.gtf.gz
+example.gtf.gz.tbi

diff --git a/debian/install b/debian/install
new file mode 100644 (file)
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--- /dev/null
+++ b/debian/install
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+tabix  usr/bin
+bgzip  usr/bin

diff --git a/debian/links b/debian/links
new file mode 100644 (file)
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--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+/usr/share/man/man1/tabix.1.gz /usr/share/man/man1/bgzip.1.gz

diff --git a/debian/manpages b/debian/manpages
new file mode 100644 (file)
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--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+tabix.1

diff --git a/debian/rules b/debian/rules
new file mode 100755 (executable)
index 0000000..dd55160
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
+
+DEB_COMPRESS_EXCLUDE  = .tbi

diff --git a/debian/source/format b/debian/source/format
new file mode 100644 (file)
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--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/debian/watch b/debian/watch
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--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+opts=downloadurlmangle=s/\/download//,filenamemangle=s/http...sourceforge.net.projects.samtools.files.tabix.//;s/.download// \
+  http://sourceforge.net/projects/samtools/files/tabix/ \
+  http://sourceforge.net/projects/samtools/files/tabix/tabix-(.*).tar.bz2/download