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debian/changelog
View file @ 3b837ed4
htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium
htsjdk (2.14.3+dfsg-1) experimental; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #894289 (FIXME: check this!)
Closes: #894289
* cme fix dpkg-control
* Standards-Version: 4.1.3
* Standards-Version: 4.1.4
* Point Vcs-fields to salsa.d.o
* Update d/copyright
* d/rules: fix get-poms target
* Use 2to3 to convert Python script to Python3
[ Olivier Sallou ]
* d/patches/30-disable-scalatest.patch
......@@ -16,11 +20,13 @@ htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium
[TODO - O. Sallou in progress]
* Reintroduce unit tests now that gradle 3.4 is available in sid
- [done] new patch added for latest upstream, referencing junit classes
- [done] added testng() call in build.gradle with a patch and set test call in d/rules back
- testng fails now with jcommander classnotfound exception, this is a testng bug
(#895886: testng: jcommander classes not found), wait to be fixed to enable tests in d/rules
- [done] added testng() call in build.gradle with a patch and set test
call in d/rules back
- testng fails now with jcommander classnotfound exception, this is a
testng bug (#895886: testng: jcommander classes not found), wait to
be fixed to enable tests in d/rules
-- Andreas Tille <tille@debian.org> Wed, 28 Mar 2018 14:19:04 +0200
-- Andreas Tille <tille@debian.org> Tue, 17 Apr 2018 15:14:40 +0200
htsjdk (2.8.1+dfsg-2) unstable; urgency=medium
......
debian/control
View file @ 3b837ed4
......@@ -24,9 +24,9 @@ Build-Depends: default-jdk (>= 2:1.8),
junit4,
libjimfs-java,
scala-library
Standards-Version: 4.1.3
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/htsjdk.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/htsjdk.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/htsjdk
Vcs-Git: https://salsa.debian.org/med-team/htsjdk.git
Homepage: http://samtools.github.io/htsjdk/
Package: libhtsjdk-java
......@@ -36,7 +36,7 @@ Depends: ${misc:Depends},
${java:Depends}
Recommends: ${java:Recommends}
Suggests: picard-tools,
python
python3
Description: Java API for high-throughput sequencing data (HTS) formats
HTSJDK is an implementation of a unified Java library for accessing common
file formats, such as SAM (Sequence Alignment/Map) and VCF, used for
......
debian/copyright
View file @ 3b837ed4
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/samtools/htsjdk/releases
Comment: Convenience binary jar files are removed.
Files-Excluded: gradle/wrapper/gradle-wrapper.jar
Files: *
Copyright: 2009-2015, The Broad Institute
Copyright: 2009-2018, The Broad Institute
License: MIT
Files: debian/*
Copyright: 2010 Shaun Jackman <sjackman@debian.org>
2013 Olivier Sallou <osallou@debian.org>
2013-2018 Olivier Sallou <osallou@debian.org>
2015 Vincent Danjean <vdanjean@debian.org>
License: ISC
Permission to use, copy, modify, and/or distribute this software for any
......@@ -18,7 +18,7 @@ License: ISC
Files: scripts/*
src/main/*
Copyright: 2009-2016, The Broad Institute
Copyright: 2009-2018, The Broad Institute
License: Expat
Files: src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java
......@@ -190,7 +190,6 @@ License: LGPL-2.1
Files: src/main/java/htsjdk/tribble/readers/AsciiLineReaderIterator.java
src/main/java/htsjdk/tribble/readers/LineIterator.java
src/main/java/htsjdk/tribble/readers/LineIteratorImpl.java
src/main/java/htsjdk/tribble/readers/LineReaderUtil.java
Copyright: 2009-2015, The Broad Institute
License: MIT
......@@ -276,10 +275,6 @@ Files: src/test/java/htsjdk/samtools/fastq/*
Copyright: 2009-2015, The Broad Institute
License: MIT
Files: src/test/java/htsjdk/samtools/fastq/FastqWriterTest.java
Copyright: 2009-2015, The Broad Institute
License: Expat
Files: src/test/java/htsjdk/samtools/filter/InsertSizeFilterTest.java
src/test/java/htsjdk/samtools/filter/MappingQualityFilterTest.java
Copyright: 2009-2015, The Broad Institute
......@@ -498,8 +493,8 @@ License: W3C-Software
date changes were made. (We recommend you provide URIs to the location
from which the code is derived).
.
In addition, creators of derivitive works must include the full text of this
NOTICE in a location viewable to users of the derivitive work.
In addition, creators of derivative works must include the full text of this
NOTICE in a location viewable to users of the derivative work.
.
THIS SOFTWARE AND DOCUMENTATION IS PROVIDED "AS IS," AND COPYRIGHT HOLDERS
MAKE NO REPRESENTATIONS OR WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT
......
debian/libhtsjdk-java.README.Debian
View file @ 3b837ed4
......@@ -8,10 +8,10 @@ reverse dependencies.
The Python script 'explain_sam_flags.py' is distributed in
'/usr/share/libhtsjdk-java/' as a convenience for the users, but
the package does not depend on it. You can install the default
Python version in Debian with the following command:
the package does not depend on it. It was converted using 2to3
from Python to Python3. You can install the default
Python3 version in Debian with the following command:
apt-get install python
-- Charles Plessy <plessy@debian.org> Tue, 06 Jul 2010 16:29:56 +0900
sudo apt-get install python3
-- Andreas Tille <tille@debian.org> Tue, 17 Apr 2018 15:14:40 +0200
debian/patches/60-enable-tests
View file @ 3b837ed4
Author: Olivier Sallou <osallou@debian.org>
Last-Update: 2018-04-17
Description: Enable tests using testng
--- a/build.gradle
+++ b/build.gradle
@@ -86,9 +86,14 @@
......
debian/patches/80-2to3.patch 0 → 100644
View file @ 3b837ed4
Author: Andreas Tille <tille@debian.org>
Last-Update: Tue, 17 Apr 2018 15:14:40 +0200
Description: Use 2to3 to convert Python script to Python3
--- a/scripts/explain_sam_flags.py
+++ b/scripts/explain_sam_flags.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
# The MIT License
#
@@ -28,7 +28,7 @@
Explain each flag on the command line in plain English
"""
-from __future__ import division
+
import sys
lstFlags = [
@@ -48,10 +48,10 @@ lstFlags = [
def explain_sam_flags(iFlags):
- print iFlags, ":"
+ print(iFlags, ":")
for strFlagName, iMask in lstFlags:
if iFlags & iMask:
- print "\t" + strFlagName
+ print("\t" + strFlagName)
def main(argv=None):
if argv is None:
debian/patches/series
View file @ 3b837ed4
......@@ -6,3 +6,4 @@
50-fix-javadoc
60-enable-tests
70-removesometests-testng.patch
80-2to3.patch
debian/rules
View file @ 3b837ed4
......@@ -21,6 +21,8 @@ override_dh_auto_test:
override_jh_installlibs:
jh_installlibs --version-strip='[+]dfsg[.0-9]*'
include /usr/share/dpkg/default.mk
# require network, not automatically run
# use it when the pom file must be re-downloaded from maven repo
BASE_URL:=https://repo.maven.apache.org/maven2/com/github/samtools/htsjdk
......@@ -29,7 +31,7 @@ WGET=wget --no-clobber
get-poms:
$(RM) debian/$(JPKG).pom debian/$(JPKG).pom.asc
# extract upstream version
VERSION=$$(dpkg-parsechangelog -S Version | sed -e 's/\([+]dfsg[.0-9]*\)\?-[^-]\+$$//') ; \
$(WGET) -O debian/$(JPKG).pom $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom && \
$(WGET) -O debian/$(JPKG).pom.asc $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom.asc
VERSION=$$(echo $(DEB_VERSION_UPSTREAM) | sed -e 's/\([+]dfsg[.0-9]*\)$$//') ; \
$(WGET) -q -O debian/$(JPKG).pom $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom && \
$(WGET) -q -O debian/$(JPKG).pom.asc $(BASE_URL)/$$VERSION/$(JPKG)-$$VERSION.pom.asc
gpg --trust-model=always --status-fd 1 --no-default-keyring --keyring debian/broadinstitute-keyring.gpg --verify debian/$(JPKG).pom.asc