broadinstitute / hellbender / 883
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lbergelson 
Merge pull request #582 from broadinstitute/lb_update_dependencies

updating dependencies

2 of 2 new or added lines in 2 files covered. (100.0%)

14707 of 20237 relevant lines covered (72.67%)

0.73 hits per line

New Missed Lines in Diff

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 src/main/java/org/broadinstitute/hellbender/tools/dataflow/MarkDuplicatesDataflow.java

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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/IntervalArgumentCollection.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/OptionalReadInputArgumentCollection.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/argumentcollections/RequiredReferenceInputArgumentCollection.java
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 src/main/java/org/broadinstitute/hellbender/engine/filters/ReadFilterLibrary.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectAlignmentSummaryMetrics.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/fastq/NormalizeFasta.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/AddOrReplaceReadGroups.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CalculateReadGroupChecksum.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/CleanSam.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceScheme.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/BQSRGatherer.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationArgumentCollection.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationTables.java
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 src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableCodec.java
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 src/main/java/org/broadinstitute/hellbender/utils/MRUCachingSAMSequenceDictionary.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/HitsForInsert.java
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 src/main/java/org/broadinstitute/hellbender/utils/text/TextFormattingUtils.java
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 src/main/java/org/broadinstitute/hellbender/exceptions/GATKException.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/ReadRecalibrationInfo.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/MergeBamAlignment.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/ContextCovariate.java
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 src/main/java/org/broadinstitute/hellbender/utils/codecs/table/TableFeature.java
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 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/TabbedTextFileWithHeaderParser.java
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 src/main/java/org/broadinstitute/hellbender/utils/variant/DbSnpBitSetUtil.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceCounts.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/QualQuantizer.java
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 src/main/java/org/broadinstitute/hellbender/transformers/BQSRReadTransformer.java
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 src/main/java/org/broadinstitute/hellbender/utils/collections/NestedIntegerArray.java
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 src/main/java/org/broadinstitute/hellbender/utils/fasta/CachingIndexedFastaSequenceFile.java
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 src/main/java/org/broadinstitute/hellbender/utils/SimpleInterval.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/markduplicates/MarkDuplicates.java
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 src/main/java/org/broadinstitute/hellbender/utils/MannWhitneyU.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/ArtificialSAMUtils.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/covariates/CycleCovariate.java
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 src/main/java/org/broadinstitute/hellbender/tools/recalibration/RecalibrationReport.java
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 src/main/java/org/broadinstitute/hellbender/utils/gene/Gene.java
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 src/main/java/org/broadinstitute/hellbender/utils/locusiterator/AlignmentStateMachine.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/SamRecordWithOrdinalAndSetDuplicateReadFlag.java
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 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/BasicInputParser.java
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 src/main/java/org/broadinstitute/hellbender/utils/text/XReadLines.java
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 src/main/java/org/broadinstitute/hellbender/engine/ReadsDataSource.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/BamToBfq.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineProgram.java
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 src/main/java/org/broadinstitute/hellbender/tools/examples/PrintReadsWithReference.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectInsertSizeMetrics.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectRrbsMetrics.java
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 src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java
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 src/main/java/org/broadinstitute/hellbender/utils/haplotype/Haplotype.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/BaseRecalibrator.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/PhysicalLocationForMateCigarSet.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordance.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/GatherVcfs.java
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 src/main/java/org/broadinstitute/hellbender/tools/walkers/bqsr/AnalyzeCovariates.java
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 src/main/java/org/broadinstitute/hellbender/utils/clipping/ReadClipper.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/FilterReads.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/QualityScoreDistribution.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/AbstractAlignmentMerger.java
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 src/main/java/org/broadinstitute/hellbender/Main.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/CigarUtils.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/markduplicates/EstimateLibraryComplexity.java
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 src/main/java/org/broadinstitute/hellbender/utils/GenomeLoc.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectBaseDistributionByCycle.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/markduplicates/PhysicalLocationForMateCigar.java
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 src/main/java/org/broadinstitute/hellbender/exceptions/UserException.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/MeanQualityByCycle.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectGcBiasMetrics.java
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 src/main/java/org/broadinstitute/hellbender/cmdline/CommandLineParser.java
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 src/main/java/org/broadinstitute/hellbender/utils/report/GATKReportTable.java
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 src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
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 src/main/java/org/broadinstitute/hellbender/utils/read/AlignmentUtils.java
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 src/main/java/org/broadinstitute/hellbender/utils/iterators/MarkDuplicatesWithMateCigarIterator.java
Jobs
ID Job ID Ran Files Coverage
1 883.1 (TERM=dumb) 0
72.67
 Travis Job 883.1
Source Files on build 883
Detailed source file information is not available for this build.