diff --git a/public/testdata/gatkrunreport.fail.xml b/public/testdata/gatkrunreport.fail.xml new file mode 100644 index 000000000..ba8228c3d --- /dev/null +++ b/public/testdata/gatkrunreport.fail.xml @@ -0,0 +1,50 @@ + + yX3AnltsqIlXH9kAQqTWHQUd8CQ5bikz + + Failed to parse Genome Location string: + 20:10,000,000-10,000,001x + + org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:377) + org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82) + org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231) + org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128) + org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) + org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) + org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92) + + + Position: '10,000,001x' contains invalid + chars. + + org.broadinstitute.sting.utils.GenomeLocParser.parsePosition(GenomeLocParser.java:411) + org.broadinstitute.sting.utils.GenomeLocParser.parseGenomeLoc(GenomeLocParser.java:374) + org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:82) + org.broadinstitute.sting.commandline.IntervalBinding.getIntervals(IntervalBinding.java:106) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.loadIntervals(GenomeAnalysisEngine.java:618) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:585) + org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:231) + org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:128) + org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236) + org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146) + org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:92) + + false + + true + + 2012/03/10 20.19.52 + 2012/03/10 20.19.52 + 0 + CountReads + 1.4-483-g63ecdb2 + 85000192 + 129957888 + depristo + 10.0.1.10 + Apple Inc.-1.6.0_26 + Mac OS X-x86_64 + 0 + diff --git a/public/testdata/gatkrunreport.success.xml b/public/testdata/gatkrunreport.success.xml new file mode 100644 index 000000000..8f89eaf46 --- /dev/null +++ b/public/testdata/gatkrunreport.success.xml @@ -0,0 +1,15 @@ + + D7D31ULwTSxlAwnEOSmW6Z4PawXwMxEz + 2012/03/10 20.21.19 + 2012/03/10 20.21.19 + 0 + CountReads + 1.4-483-g63ecdb2 + 85000192 + 129957888 + depristo + 10.0.1.10 + Apple Inc.-1.6.0_26 + Mac OS X-x86_64 + 105 +