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Demonstrate errors reported in issue #27 #44

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@heuermh heuermh commented Oct 3, 2018

This pull request will fail to build. It demonstrates the errors reported in issue #27.

$ mvn clean install
...
Tests in error:
  testReadAndWrite(1.bam, null, BAM, 131072, false) [0](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(1.bam, null, BAM, 131072, true) [1](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(test.sam, null, SAM, 131072, false) [5](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(gs://genomics-public-data/NA12878.chr20.sample.bam, null, BAM, 131072, true) [6](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(gs://genomics-public-data/NA12878.chr20.sample.bam, null, BAM, 0, true) [7](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam/part-r-00000.bam, null, BAM, 76458, false) [8](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(HiSeq.1mb.1RG.2k_lines.alternate.recalibrated.DIQ.sharded.bam/part-r-00000.bam, null, BAM, 76458, true) [9](org.disq_bio.disq.HtsjdkReadsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.UnsupportedOperationException(..)
  testReadAndWrite(test.vcf, VCF, 131072) [0](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)
  testReadAndWrite(test.vcf, VCF_GZ, 131072) [1](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)
  testReadAndWrite(test.vcf, VCF_BGZ, 131072) [2](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)
  testReadAndWrite(test.vcf.bgz, VCF, 131072) [3](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)
  testReadAndWrite(test.vcf.bgzf.gz, VCF, 131072) [4](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)
  testReadAndWrite(test.vcf.gz, VCF, 131072) [5](org.disq_bio.disq.HtsjdkVariantsRddTest):
Job aborted due to stage failure: Exception while getting task result:
com.esotericsoftware.kryo.KryoException: java.lang.NullPointerException(..)

Tests run: 57, Failures: 0, Errors: 13, Skipped: 1

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------

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heuermh commented Oct 24, 2018

Closing in favor of #52.

@heuermh heuermh closed this Oct 24, 2018
@heuermh heuermh deleted the issue-27 branch October 24, 2018 17:03
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