Class org.broadinstitute.hellbender.testutils.IntegrationTestSpecUnitTest

all > org.broadinstitute.hellbender.testutils > IntegrationTestSpecUnitTest

tests

failures

ignored

0.017s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
compareEqualTextFiles	0.001s	passed
compareFilesWithAndWithoutComments[0](fileWithComments.txt, fileWithNoComments.txt)	0.006s	passed
compareFilesWithAndWithoutComments[1](fileWithComments.txt, fileWithDifferentComments.txt)	0s	passed
compareFilesWithAndWithoutComments[2](fileWithNoComments.txt, fileWithComments.txt)	0.001s	passed
compareFilesWithAndWithoutComments[3](fileWithNoComments.txt, fileWithDifferentComments.txt)	0s	passed
compareFilesWithAndWithoutComments_ignoreComments[0](fileWithComments.txt, fileWithNoComments.txt)	0s	passed
compareFilesWithAndWithoutComments_ignoreComments[1](fileWithComments.txt, fileWithDifferentComments.txt)	0.001s	passed
compareFilesWithAndWithoutComments_ignoreComments[2](fileWithNoComments.txt, fileWithComments.txt)	0s	passed
compareFilesWithAndWithoutComments_ignoreComments[3](fileWithNoComments.txt, fileWithDifferentComments.txt)	0s	passed
compareTextFiles	0.003s	passed
compareTextFiles_differentEvenIgnoringComments	0.004s	passed
testSpec_misspecified	0.001s	passed

Standard output

--------------------------------------------------------------------------------

Standard error

20:25:28.799 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected this is some content actual #This is a different comment
Expected :this is some content
Actual   :#This is a different comment

20:25:28.799 ERROR IntegrationTestSpec - Line number 1 (not counting comments) expected this is some other content actual #This is a comment too
Expected :this is some other content
Actual   :#This is a comment too

20:25:28.801 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected #This is a comment actual #This is a different comment
Expected :#This is a comment
Actual   :#This is a different comment

20:25:28.801 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected #This is a different comment actual this is some content
Expected :#This is a different comment
Actual   :this is some content

20:25:28.801 ERROR IntegrationTestSpec - Line number 1 (not counting comments) expected #This is a comment too actual this is some other content
Expected :#This is a comment too
Actual   :this is some other content

20:25:28.802 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected #This is a comment actual this is some content
Expected :#This is a comment
Actual   :this is some content

20:25:28.802 ERROR IntegrationTestSpec - Line number 1 (not counting comments) expected #This is a comment too actual this is some other content
Expected :#This is a comment too
Actual   :this is some other content

20:25:28.803 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected [![Build Status](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml/badge.svg?branch=master)](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml) actual # This is the official list of GATK authors for copyright purposes.
Expected :[![Build Status](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml/badge.svg?branch=master)](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml)
Actual   :# This is the official list of GATK authors for copyright purposes.

20:25:28.804 ERROR IntegrationTestSpec - Line number 1 (not counting comments) expected [![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk) actual #
Expected :[![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk)
Actual   :#

20:25:28.804 ERROR IntegrationTestSpec - Line number 2 (not counting comments) expected [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) actual # The AUTHORS file lists the copyright holders.
Expected :[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
Actual   :# The AUTHORS file lists the copyright holders.

20:25:28.804 ERROR IntegrationTestSpec - Line number 3 (not counting comments) expected ***Please see the [GATK website](http://www.broadinstitute.org/gatk), where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see [here](https://software.broadinstitute.org/gatk/documentation/article?id=23405).*** actual # For example, Broad Institute employees are not listed here,
Expected :***Please see the [GATK website](http://www.broadinstitute.org/gatk), where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see [here](https://software.broadinstitute.org/gatk/documentation/article?id=23405).***
Actual   :# For example, Broad Institute employees are not listed here,

20:25:28.804 ERROR IntegrationTestSpec - Line number 4 (not counting comments) expected ### GATK 4 actual # because Broad Institute holds the copyright.
Expected :### GATK 4
Actual   :# because Broad Institute holds the copyright.

20:25:28.804 ERROR IntegrationTestSpec - Line number 5 (not counting comments) expected This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents actual # Names should be added to this file as
Expected :This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents
Actual   :# Names should be added to this file as

20:25:28.804 ERROR IntegrationTestSpec - Line number 6 (not counting comments) expected of this repository are 100% open source and released under the Apache 2.0 license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)). actual # Organization <webpage>
Expected :of this repository are 100% open source and released under the Apache 2.0 license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)).
Actual   :# Organization <webpage>

20:25:28.804 ERROR IntegrationTestSpec - Line number 7 (not counting comments) expected GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and actual # Individual Name <email address or website>
Expected :GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and
Actual   :# Individual Name <email address or website>

20:25:28.804 ERROR IntegrationTestSpec - Line number 8 (not counting comments) expected [Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework, actual # Please keep the list sorted alphabetically, companies/organizations first, individuals second.
Expected :[Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework,
Actual   :# Please keep the list sorted alphabetically, companies/organizations first, individuals second.

20:25:28.804 ERROR IntegrationTestSpec - Line number 9 (not counting comments) expected and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using actual Broad Institute, Inc. <www.broadinstitute.org>
Expected :and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using
Actual   :Broad Institute, Inc. <www.broadinstitute.org>

20:25:28.804 ERROR IntegrationTestSpec - Line number 10 (not counting comments) expected [Apache Spark](http://spark.apache.org/). It also contains many newly developed tools not present in earlier actual Cloudera Inc. <www.cloudera.com>
Expected :[Apache Spark](http://spark.apache.org/). It also contains many newly developed tools not present in earlier
Actual   :Cloudera Inc. <www.cloudera.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 11 (not counting comments) expected releases of the toolkit. actual Google Inc. <www.google.com>
Expected :releases of the toolkit.
Actual   :Google Inc. <www.google.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 12 (not counting comments) expected ## Table of Contents actual IBM Corp <www.ibm.com>
Expected :## Table of Contents
Actual   :IBM Corp <www.ibm.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 13 (not counting comments) expected * [Requirements](#requirements) actual Intel Corp. <www.intel.com>
Expected :* [Requirements](#requirements)
Actual   :Intel Corp. <www.intel.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 14 (not counting comments) expected * [Quick Start Guide](#quickstart) actual Anders Peterson <apete@optimatika.se>
Expected :* [Quick Start Guide](#quickstart)
Actual   :Anders Peterson <apete@optimatika.se>

20:25:28.804 ERROR IntegrationTestSpec - Line number 15 (not counting comments) expected * [Downloading GATK4](#downloading) actual Axel Verdier <axel.verdier@inra.fr>
Expected :* [Downloading GATK4](#downloading)
Actual   :Axel Verdier <axel.verdier@inra.fr>

20:25:28.804 ERROR IntegrationTestSpec - Line number 16 (not counting comments) expected * [Tools Included in Docker Image](#dockerSoftware) actual Ayman Abdel Ghany <aymana.ghany@devfactory.com>
Expected :* [Tools Included in Docker Image](#dockerSoftware)
Actual   :Ayman Abdel Ghany <aymana.ghany@devfactory.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 17 (not counting comments) expected * [Building GATK4](#building) actual Ben Bimber <bimber@ohsu.edu>
Expected :* [Building GATK4](#building)
Actual   :Ben Bimber <bimber@ohsu.edu>

20:25:28.804 ERROR IntegrationTestSpec - Line number 18 (not counting comments) expected * [Running GATK4](#running) actual Byunggil Yoo <byunggil.yoo@gmail.com>
Expected :* [Running GATK4](#running)
Actual   :Byunggil Yoo <byunggil.yoo@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 19 (not counting comments) expected * [Passing JVM options to gatk](#jvmoptions) actual Daniel Gómez-Sánchez <daniel.gomez.sanchez@hotmail.es>
Expected :* [Passing JVM options to gatk](#jvmoptions)
Actual   :Daniel Gómez-Sánchez <daniel.gomez.sanchez@hotmail.es>

20:25:28.804 ERROR IntegrationTestSpec - Line number 20 (not counting comments) expected * [Passing a configuration file to gatk](#configFileOptions) actual Don Freed <donfreed12@gmail.com>
Expected :* [Passing a configuration file to gatk](#configFileOptions)
Actual   :Don Freed <donfreed12@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 21 (not counting comments) expected * [Running GATK4 with inputs on Google Cloud Storage](#gcs) actual Eugene Wolfson <evulfson@gmail.com>
Expected :* [Running GATK4 with inputs on Google Cloud Storage](#gcs)
Actual   :Eugene Wolfson <evulfson@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 22 (not counting comments) expected * [Running GATK4 Spark tools locally](#sparklocal) actual Frank Austin Nothaft <frank.nothaft@databricks.com>
Expected :* [Running GATK4 Spark tools locally](#sparklocal)
Actual   :Frank Austin Nothaft <frank.nothaft@databricks.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 23 (not counting comments) expected * [Running GATK4 Spark tools on a Spark cluster](#sparkcluster) actual Jake VanCampen <jake.vancampen7@gmail.com>
Expected :* [Running GATK4 Spark tools on a Spark cluster](#sparkcluster)
Actual   :Jake VanCampen <jake.vancampen7@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 24 (not counting comments) expected * [Running GATK4 Spark tools on Google Cloud Dataproc](#dataproc) actual Josh Holland <anowlcalledjosh@gmail.com>
Expected :* [Running GATK4 Spark tools on Google Cloud Dataproc](#dataproc)
Actual   :Josh Holland <anowlcalledjosh@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 25 (not counting comments) expected * [Using R to generate plots](#R) actual Kenji Kaneda <kenji.kaneda@gmail.com>
Expected :* [Using R to generate plots](#R)
Actual   :Kenji Kaneda <kenji.kaneda@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 26 (not counting comments) expected * [GATK Tab Completion for Bash](#tab_completion) actual Kohl Kinning <kohlkinning@gmail.com>
Expected :* [GATK Tab Completion for Bash](#tab_completion)
Actual   :Kohl Kinning <kohlkinning@gmail.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 27 (not counting comments) expected * [For GATK Developers](#developers) actual Mohammed Ezzat <mohamed.ezzat@devfactory.com>
Expected :* [For GATK Developers](#developers)
Actual   :Mohammed Ezzat <mohamed.ezzat@devfactory.com>

20:25:28.804 ERROR IntegrationTestSpec - Line number 28 (not counting comments) expected * [General guidelines for GATK4 developers](#dev_guidelines) actual Nicholas Newell <nenewell@comcast.net>
Expected :* [General guidelines for GATK4 developers](#dev_guidelines)
Actual   :Nicholas Newell <nenewell@comcast.net>

20:25:28.804 ERROR IntegrationTestSpec - Line number 29 (not counting comments) expected * [Testing GATK4](#testing) actual Nils Homer <nilshomer@gmail.com>
Expected :* [Testing GATK4](#testing)
Actual   :Nils Homer <nilshomer@gmail.com>

20:25:28.805 ERROR IntegrationTestSpec - Line number 30 (not counting comments) expected * [Using Git LFS to download and track large test data](#lfs) actual Tim Fennell <tfenne@tfenne.com>
Expected :* [Using Git LFS to download and track large test data](#lfs)
Actual   :Tim Fennell <tfenne@tfenne.com>

20:25:28.806 ERROR IntegrationTestSpec - Line number 0 (not counting comments) expected [![Build Status](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml/badge.svg?branch=master)](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml) actual Broad Institute, Inc. <www.broadinstitute.org>
Expected :[![Build Status](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml/badge.svg?branch=master)](https://github.com/broadinstitute/gatk/actions/workflows/gatk-tests.yml)
Actual   :Broad Institute, Inc. <www.broadinstitute.org>

20:25:28.806 ERROR IntegrationTestSpec - Line number 1 (not counting comments) expected [![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk) actual Cloudera Inc. <www.cloudera.com>
Expected :[![Maven Central](https://img.shields.io/maven-central/v/org.broadinstitute/gatk.svg)](https://maven-badges.herokuapp.com/maven-central/org.broadinstitute/gatk)
Actual   :Cloudera Inc. <www.cloudera.com>

20:25:28.806 ERROR IntegrationTestSpec - Line number 2 (not counting comments) expected [![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0) actual Google Inc. <www.google.com>
Expected :[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
Actual   :Google Inc. <www.google.com>

20:25:28.806 ERROR IntegrationTestSpec - Line number 3 (not counting comments) expected ***Please see the [GATK website](http://www.broadinstitute.org/gatk), where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see [here](https://software.broadinstitute.org/gatk/documentation/article?id=23405).*** actual IBM Corp <www.ibm.com>
Expected :***Please see the [GATK website](http://www.broadinstitute.org/gatk), where you can download a precompiled executable, read documentation, ask questions, and receive technical support. For GitHub basics, see [here](https://software.broadinstitute.org/gatk/documentation/article?id=23405).***
Actual   :IBM Corp <www.ibm.com>

20:25:28.806 ERROR IntegrationTestSpec - Line number 4 (not counting comments) expected This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents actual Intel Corp. <www.intel.com>
Expected :This repository contains the next generation of the Genome Analysis Toolkit (GATK). The contents
Actual   :Intel Corp. <www.intel.com>

20:25:28.806 ERROR IntegrationTestSpec - Line number 5 (not counting comments) expected of this repository are 100% open source and released under the Apache 2.0 license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)). actual Anders Peterson <apete@optimatika.se>
Expected :of this repository are 100% open source and released under the Apache 2.0 license (see [LICENSE.TXT](https://github.com/broadinstitute/gatk/blob/master/LICENSE.TXT)).
Actual   :Anders Peterson <apete@optimatika.se>

20:25:28.807 ERROR IntegrationTestSpec - Line number 6 (not counting comments) expected GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and actual Axel Verdier <axel.verdier@inra.fr>
Expected :GATK4 aims to bring together well-established tools from the [GATK](http://www.broadinstitute.org/gatk) and
Actual   :Axel Verdier <axel.verdier@inra.fr>

20:25:28.807 ERROR IntegrationTestSpec - Line number 7 (not counting comments) expected [Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework, actual Ayman Abdel Ghany <aymana.ghany@devfactory.com>
Expected :[Picard](http://broadinstitute.github.io/picard/) codebases under a streamlined framework,
Actual   :Ayman Abdel Ghany <aymana.ghany@devfactory.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 8 (not counting comments) expected and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using actual Ben Bimber <bimber@ohsu.edu>
Expected :and to enable selected tools to be run in a massively parallel way on local clusters or in the cloud using
Actual   :Ben Bimber <bimber@ohsu.edu>

20:25:28.807 ERROR IntegrationTestSpec - Line number 9 (not counting comments) expected [Apache Spark](http://spark.apache.org/). It also contains many newly developed tools not present in earlier actual Byunggil Yoo <byunggil.yoo@gmail.com>
Expected :[Apache Spark](http://spark.apache.org/). It also contains many newly developed tools not present in earlier
Actual   :Byunggil Yoo <byunggil.yoo@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 10 (not counting comments) expected releases of the toolkit. actual Daniel Gómez-Sánchez <daniel.gomez.sanchez@hotmail.es>
Expected :releases of the toolkit.
Actual   :Daniel Gómez-Sánchez <daniel.gomez.sanchez@hotmail.es>

20:25:28.807 ERROR IntegrationTestSpec - Line number 11 (not counting comments) expected * [Requirements](#requirements) actual Don Freed <donfreed12@gmail.com>
Expected :* [Requirements](#requirements)
Actual   :Don Freed <donfreed12@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 12 (not counting comments) expected * [Quick Start Guide](#quickstart) actual Eugene Wolfson <evulfson@gmail.com>
Expected :* [Quick Start Guide](#quickstart)
Actual   :Eugene Wolfson <evulfson@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 13 (not counting comments) expected * [Downloading GATK4](#downloading) actual Frank Austin Nothaft <frank.nothaft@databricks.com>
Expected :* [Downloading GATK4](#downloading)
Actual   :Frank Austin Nothaft <frank.nothaft@databricks.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 14 (not counting comments) expected * [Tools Included in Docker Image](#dockerSoftware) actual Jake VanCampen <jake.vancampen7@gmail.com>
Expected :* [Tools Included in Docker Image](#dockerSoftware)
Actual   :Jake VanCampen <jake.vancampen7@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 15 (not counting comments) expected * [Building GATK4](#building) actual Josh Holland <anowlcalledjosh@gmail.com>
Expected :* [Building GATK4](#building)
Actual   :Josh Holland <anowlcalledjosh@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 16 (not counting comments) expected * [Running GATK4](#running) actual Kenji Kaneda <kenji.kaneda@gmail.com>
Expected :* [Running GATK4](#running)
Actual   :Kenji Kaneda <kenji.kaneda@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 17 (not counting comments) expected * [Passing JVM options to gatk](#jvmoptions) actual Kohl Kinning <kohlkinning@gmail.com>
Expected :* [Passing JVM options to gatk](#jvmoptions)
Actual   :Kohl Kinning <kohlkinning@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 18 (not counting comments) expected * [Passing a configuration file to gatk](#configFileOptions) actual Mohammed Ezzat <mohamed.ezzat@devfactory.com>
Expected :* [Passing a configuration file to gatk](#configFileOptions)
Actual   :Mohammed Ezzat <mohamed.ezzat@devfactory.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 19 (not counting comments) expected * [Running GATK4 with inputs on Google Cloud Storage](#gcs) actual Nicholas Newell <nenewell@comcast.net>
Expected :* [Running GATK4 with inputs on Google Cloud Storage](#gcs)
Actual   :Nicholas Newell <nenewell@comcast.net>

20:25:28.807 ERROR IntegrationTestSpec - Line number 20 (not counting comments) expected * [Running GATK4 Spark tools locally](#sparklocal) actual Nils Homer <nilshomer@gmail.com>
Expected :* [Running GATK4 Spark tools locally](#sparklocal)
Actual   :Nils Homer <nilshomer@gmail.com>

20:25:28.807 ERROR IntegrationTestSpec - Line number 21 (not counting comments) expected * [Running GATK4 Spark tools on a Spark cluster](#sparkcluster) actual Tim Fennell <tfenne@tfenne.com>
Expected :* [Running GATK4 Spark tools on a Spark cluster](#sparkcluster)
Actual   :Tim Fennell <tfenne@tfenne.com>