search

lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
Other
487 stars 133 forks source link

vcf2svg #222

Open Shingzzz opened 2 years ago

Shingzzz commented 2 years ago

output:

Initialized native services in: /root/.gradle/native
Initialized jansi services in: /root/.gradle/native
The client will now receive all logging from the daemon (pid: 20895). The daemon log file: /root/.gradle/daemon/7.4.2/daemon-20895.out.log
Starting 3rd build in daemon [uptime: 1 hrs 26 mins 53.363 secs, performance: 100%, non-heap usage: 17% of 256 MiB]
Using 2 worker leases.
Watching the file system is configured to be enabled if available
File system watching is inactive
Starting Build
Settings evaluated using settings file '/root/hpc/jvarkit/settings.gradle'.
Projects loaded. Root project using build file '/root/hpc/jvarkit/build.gradle'.
Included projects: [root project 'jvarkit']

> Configure project :
Evaluating root project 'jvarkit' using build file '/root/hpc/jvarkit/build.gradle'.
All projects evaluated.
Selected primary task 'vcf2svg' from project :
Tasks to be executed: [vcf2svg com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvg]
Tasks that were excluded: []
:vcf2svg (Thread[included builds,5,main]) started.
[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8

> Task :vcf2svg
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
Caching disabled for vcf2svg com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvg because:
  Build cache is disabled
Vcf2svg com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvg is not up-to-date because:
  Task has not declared any outputs despite executing actions.
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/vcf2svg
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which java
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which javac
Successfully started process 'command 'which''
Starting process 'command 'which''. Working directory: /root/hpc/jvarkit Command: which jar
Successfully started process 'command 'which''
[ant:javac] Compiling 1 source file to /root/hpc/jvarkit/tmp

[ant:javac] 1 warning

> Task :vcf2svg
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/com/github/lindenb/jvarkit/tools/vcf2svg
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:copy] Copying 1 file to /root/hpc/jvarkit/tmp/META-INF/chromnames
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/github/samtools/htsjdk/3.0.0/htsjdk-3.0.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/commons-logging/commons-logging/1.1.1/commons-logging-1.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/gov/nih/nlm/ncbi/ngs-java/2.9.0/ngs-java-2.9.0.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-jexl/2.1.1/commons-jexl-2.1.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/apache/commons/commons-compress/1.19/commons-compress-1.19.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/tukaani/xz/1.8/xz-1.8.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/sharegov/mjson/1.4.1/mjson-1.4.1.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/org/xerial/snappy/snappy-java/1.1.8.4/snappy-java-1.1.8.4.jar into /root/hpc/jvarkit/tmp
[ant:unzip] Expanding: /root/hpc/jvarkit/lib/com/beust/jcommander/1.72/jcommander-1.72.jar into /root/hpc/jvarkit/tmp
Starting process 'command 'git''. Working directory: /root/hpc/jvarkit Command: git rev-parse --short HEAD
Successfully started process 'command 'git''
[ant:jar] Building jar: /root/hpc/jvarkit/dist/vcf2svg.jar
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp
jar file generated :/root/hpc/jvarkit/dist/vcf2svg.jar
[ant:mkdir] Created dir: /root/hpc/jvarkit/tmp
Test will be executed in /root/hpc/jvarkit/tests-output/vcf2svg/index.html
[ant:javac] Compiling 2 source files to /root/hpc/jvarkit/tmp

[ant:javac] warning: [options] bootstrap class path not set in conjunction with -source 8
[ant:javac] 1 warning
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvgTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.jcommander.LauncherTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.io.IOUtilsTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.LineIteratorsTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.StringUtilsTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.AbstractCharSequenceTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.DelegateCharSequenceTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.VCFUtilsTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.CharSplitterTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.SequenceDictionaryUtilsTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.fasta.ContigNameConverterTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.IntervalParserFactoryTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.util.SimpleIntervalTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.vcf.AFExtractorFactoryTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.tools.vcftrios.DeNovoDetectorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.CounterTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.bed.BedLineCodecTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.log.ProgressFactoryTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.samtools.ContigDictComparatorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.SmartComparatorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.EqualRangeIteratorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.FilterIteratorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.iterator.MergingIteratorTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.util.bio.samfilter.SamRecordFilterFactoryTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.samtools.reference.TwoBitSequenceFileTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.math.DiscreteMedianTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.IntArrayTest
[ant:java] Nov 18, 2022 1:12:15 PM com.github.lindenb.jvarkit.tools.tests.MiniTestNG registerTestClass
[ant:java] INFO: adding class com.github.lindenb.jvarkit.lang.primitive.DoubleArrayTest
[ant:java] There was an error in the input parameters: The following option is required: [-r | --interval]
[ant:java] [TEST] end TestSupport
[ant:java] There was an error in the input parameters: The following option is required: [-r | --interval]
[ant:java] [TEST] end TestSupport
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java] [WARN][AFExtractorFactory]VCF header doesn't contain the INFO field x_AC
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:3 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=45. That took:1 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=11. That took:10 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=477. That took:28 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:38 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:22 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:9 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:9 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=1,998. That took:8 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:0 millisecs
[ant:java] [INFO][ProgressFactory]. Completed. N=12. That took:7 millisecs
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] [TEST] end TestSupport
[ant:java] 
[ant:java] ===============================================
[ant:java] Command line suite
[ant:java] Total tests run: 100, Failures: 2, Skips: 0
[ant:java] ===============================================
[ant:java] 
[ant:java] [TEST] end TestSupport

> Task :vcf2svg
[ant:java] Java Result: 255
[ant:delete] Deleting directory /root/hpc/jvarkit/tmp
:vcf2svg (Thread[included builds,5,main]) completed. Took 10.472 secs.

BUILD SUCCESSFUL in 11s
1 actionable task: 1 executed

2 tests failed, the tests-output\vcf2svg\index.html shows:

Failed methods :
 testVcfToSvg
 testVcfToSvgManifest

testVcfToSvg
java.lang.AssertionError: expected [-1] but found [0]
    at com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvgTest.testVcfToSvg(VcfToSvgTest.java:31)
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
... Removed 28 stack frames
testVcfToSvgManifest
java.lang.AssertionError: expected [-1] but found [0]
    at com.github.lindenb.jvarkit.tools.vcf2svg.VcfToSvgTest.testVcfToSvgManifest(VcfToSvgTest.java:52)
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.doWork(MiniTestNG.java:77)
    at com.github.lindenb.jvarkit.tools.tests.MiniTestNG.main(MiniTestNG.java:87)
... Removed 28 stack frames

why this part expected -1 ？I see the VcfToSvgTest.java:31 is Assert.assertEquals(0,