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analyzeRunReports cleanup for new minimal GATKRunReport structure 

-- No more command lines or working directories
-- Added failing and successful gatkrunreports to public/testdata for testing
This commit is contained in:
Mark DePristo 2012-03-11 10:41:29 -04:00
parent 03223029e3
commit a63d1f58b6
2 changed files with 65 additions and 0 deletions
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50
public/testdata/gatkrunreport.fail.xml vendored 100644
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<GATK-run-report>
<id>yX3AnltsqIlXH9kAQqTWHQUd8CQ5bikz</id>
<exception>
<message>Failed to parse Genome Location string:
20:10,000,000-10,000,001x</message>
<stacktrace class="java.util.ArrayList">
<string>org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:377)</string>
<string>org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82)</string>
<string>org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231)</string>
<string>org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)</string>
<string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)</string>
<string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)</string>
<string>org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)</string>
</stacktrace>
<cause>
<message>Position: &apos;10,000,001x&apos; contains invalid
chars.</message>
<stacktrace class="java.util.ArrayList">
<string>org.broadinstitute.sting.utils.GenomeLocParser.parsePosition(GenomeLocParser.java:411)</string>
<string>org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:374)</string>
<string>org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82)</string>
<string>org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585)</string>
<string>org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231)</string>
<string>org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128)</string>
<string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)</string>
<string>org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)</string>
<string>org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92)</string>
</stacktrace>
<is-user-exception>false</is-user-exception>
</cause>
<is-user-exception>true</is-user-exception>
</exception>
<start-time>2012/03/10 20.19.52</start-time>
<end-time>2012/03/10 20.19.52</end-time>
<run-time>0</run-time>
<walker-name>CountReads</walker-name>
<svn-version>1.4-483-g63ecdb2</svn-version>
<total-memory>85000192</total-memory>
<max-memory>129957888</max-memory>
<user-name>depristo</user-name>
<host-name>10.0.1.10</host-name>
<java>Apple Inc.-1.6.0_26</java>
<machine>Mac OS X-x86_64</machine>
<iterations>0</iterations>
</GATK-run-report>

15
public/testdata/gatkrunreport.success.xml vendored 100644
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<GATK-run-report>
<id>D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz</id>
<start-time>2012/03/10 20.21.19</start-time>
<end-time>2012/03/10 20.21.19</end-time>
<run-time>0</run-time>
<walker-name>CountReads</walker-name>
<svn-version>1.4-483-g63ecdb2</svn-version>
<total-memory>85000192</total-memory>
<max-memory>129957888</max-memory>
<user-name>depristo</user-name>
<host-name>10.0.1.10</host-name>
<java>Apple Inc.-1.6.0_26</java>
<machine>Mac OS X-x86_64</machine>
<iterations>105</iterations>
</GATK-run-report>