Commit 5eec480f authored by Andreas Tille's avatar Andreas Tille

New upstream version 2.8.1+dfsg

parent 06555f99

Too many changes to show.

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### Verify
Can you see anything in the logs?
Make sure your issue is not already in the [htsjdk issue tracker](https://github.com/samtools/htsjdk/issues?q=)
### Subject of the issue
Describe your issue here.
Provide **screenshots** , **stacktrace** , **logs** where appropriate.
### Your environment
* version of htsjdk
* version of java
* which OS
### Steps to reproduce
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### Expected behaviour
Tell us what should happen
### Actual behaviour
Tell us what happens instead
### Description
Please explain the changes you made here.
Explain the **motivation** for making this change. What existing problem does the pull request solve?
### Checklist
- [ ] Code compiles correctly
- [ ] New tests covering changes and new functionality
- [ ] All tests passing
- [ ] Extended the README / documentation, if necessary
- [ ] Is not backward compatible (breaks binary or source compatibility)
htsjdk.iws
.command_tmp
atlassian-ide-plugin.xml
/htsjdk.version.properties
/test-output
#intellij
.idea/
src/htsjdk.iml
*.iml
*.ipr
*.iws
#gradle stuff
.gradle/
build/
*~
.DS_Store
._*
*.d
*.db
*.o
*.pyc
/bin64
/build/BUILD.*
/build/COMP.mac
/centos
/ilib64
/lib64
/mac
/Makefile.config.*
/reconfigure
/schema
/test-bin64
/win
*.log
/.cproject
/.project
/.pydevproject
language: java
dist: trusty
sudo: true
before_cache:
- rm -f $HOME/.gradle/caches/modules-2/modules-2.lock
cache:
directories:
- $HOME/.gradle/caches/
- $HOME/.gradle/wrapper/
- $HOME/.m2
jdk:
- oraclejdk8
script: ./gradlew jacocoTestReport testSRA;
after_success:
- echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";
echo "JAVA_HOME='$JAVA_HOME'";
./gradlew coveralls;
if [ "$TRAVIS_BRANCH" == "master" ]; then
./gradlew uploadArchives;
fi
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CONTENTS
Public Domain Notice
Exceptions (for bundled 3rd-party code)
Copyright F.A.Q.
==============================================================
PUBLIC DOMAIN NOTICE
National Center for Biotechnology Information
With the exception of certain third-party files summarized below, this
software is a "United States Government Work" under the terms of the
United States Copyright Act. It was written as part of the authors'
official duties as United States Government employees and thus cannot
be copyrighted. This software is freely available to the public for
use. The National Library of Medicine and the U.S. Government have not
placed any restriction on its use or reproduction.
Although all reasonable efforts have been taken to ensure the accuracy
and reliability of the software and data, the NLM and the U.S.
Government do not and cannot warrant the performance or results that
may be obtained by using this software or data. The NLM and the U.S.
Government disclaim all warranties, express or implied, including
warranties of performance, merchantability or fitness for any
particular purpose.
Please cite the authors in any work or product based on this material.
==============================================================
EXCEPTIONS (in all cases excluding NCBI-written makefiles):
See LICENSE from https://github.com/ncbi/ncbi-vdb
==============================================================
Copyright F.A.Q.
--------------------------------------------------------------
Q. Our product makes use of the NCBI source code, and we made changes
and additions to that version of the NCBI code to better fit it to
our needs. Can we copyright the code, and how?
A. You can copyright only the *changes* or the *additions* you made to the
NCBI source code. You should identify unambiguously those sections of
the code that were modified, e.g. by commenting any changes you made
in the code you distribute. Therefore, your license has to make clear
to users that your product is a combination of code that is public domain
within the U.S. (but may be subject to copyright by the U.S. in foreign
countries) and code that has been created or modified by you.
--------------------------------------------------------------
Q. Can we (re)license all or part of the NCBI source code?
A. No, you cannot license or relicense the source code written by NCBI
since you cannot claim any copyright in the software that was developed
at NCBI as a 'government work' and consequently is in the public domain
within the U.S.
--------------------------------------------------------------
Q. What if these copyright guidelines are not clear enough or are not
applicable to my particular case?
A. Contact us. Send your questions to 'sra-tools@ncbi.nlm.nih.gov'.
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#-------------------------------------------------------------------------------
# environment
#
TOP ?= $(CURDIR)
include $(TOP)/build/Makefile.shell
#-------------------------------------------------------------------------------
# default
#
SUBDIRS = \
shared \
tools \
# common targets for non-leaf Makefiles; must follow a definition of SUBDIRS
include $(TOP)/build/Makefile.targets
default: $(SUBDIRS)
test: all
$(SUBDIRS) test:
@ $(MAKE) -C $@
.PHONY: default $(SUBDIRS) test
#-------------------------------------------------------------------------------
# all
#
$(SUBDIRS_ALL):
#-------------------------------------------------------------------------------
# std
#
$(SUBDIRS_STD):
#-------------------------------------------------------------------------------
# install
#
install:
@ echo "Checking make status of tools..."
@ $(MAKE) -s --no-print-directory TOP=$(CURDIR) std
@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install install
uninstall:
@ $(MAKE) -s TOP=$(CURDIR) -f build/Makefile.install uninstall
.PHONY: install uninstall
#-------------------------------------------------------------------------------
# clean
#
clean: clean_deb clean_rpm clean_test
clean_test:
<