broadinstitute / hellbender / 850
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mattsooknah 
Merge pull request #347 from broadinstitute/mds_port_all_the_things

Porting the rest of Picard

8574 of 8574 new or added lines in 179 files covered. (100.0%)

15756 of 22765 relevant lines covered (69.21%)

0.69 hits per line

New Missed Lines in Diff

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/BaseDistributionByCycleMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/GcBiasDetailMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/GcBiasSummaryMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/Transition.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/HsMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/JumpingLibraryMetrics.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/TargetMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/TargetedPcrMetrics.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/ClusterDataToSamConverter.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaFileMap.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaMetricsCode.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ParameterizedFileUtil.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ReadDescriptor.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/Tile.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/BclFileFaker.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/MultiTileLocsFileFaker.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/BarcodeFileReader.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/PosFileReader.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/UpdateVcfSequenceDictionary.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfFormatConverter.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/ByIntervalListVariantContextIterator.java
1
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/QdFilter.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/walkers/rnaseq/SplitNCigarReads.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/MathUtils.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/UnsignedTypeUtil.java
1
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 src/main/java/org/broadinstitute/hellbender/utils/gene/GeneAnnotationReader.java
1
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/BasicInputParser.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectAlignmentSummaryMetrics.java
2
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ArtifactCounter.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/SequencingArtifactMetrics.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/metrics/CollectIlluminaBasecallingMetrics.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/metrics/CollectIlluminaLaneMetrics.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/CycleIlluminaFileMap.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaParserException.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/BciFileFaker.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/FileFaker.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/ClocsFileReader.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/interval/BedToIntervalList.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/interval/IntervalListScatterer.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ReorderSam.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/filter/FilterApplyingVariantIterator.java
2
100.0
 src/main/java/org/broadinstitute/hellbender/utils/illumina/ClippingUtil.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/AlignmentSummaryMetricsCollector.java
3
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IntensityChannel.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/FilterFileReader.java
3
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SortVcf.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/InsertSizeMetricsCollector.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/SinglePassSamProgram.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ContextAccumulator.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectRnaSeqMetrics.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectTargetedPcrMetrics.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/BarcodeParser.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/BclParser.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/FilterParser.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/TileMetricsUtil.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/PosFileFaker.java
4
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SplitVcfs.java
4
100.0
 src/main/java/org/broadinstitute/hellbender/utils/gene/GeneAnnotationException.java
5
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectRrbsMetrics.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/TargetedPcrMetricsCollector.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaFileUtil.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/PerTileFileUtil.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/PerTileParser.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/PosParser.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceScheme.java
5
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/CsvInputParser.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectInsertSizeMetrics.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/CollectSequencingArtifactMetrics.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/Range.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ReadData.java
6
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/LocsFileReader.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/metrics/IlluminaBasecallingMetrics.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfToIntervalList.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/AbstractInputParser.java
7
100.0
 src/main/java/org/broadinstitute/hellbender/utils/text/parsers/TabbedTextFileWithHeaderParser.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/OutputMapping.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/PerTileCycleParser.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/ClocsFileFaker.java
8
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/LocsFileFaker.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileFileUtil.java
9
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileFilterParser.java
10
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 src/main/java/org/broadinstitute/hellbender/metrics/MultiLevelCollector.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/fakers/MultiTileBclFileFaker.java
10
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/TileMetricsOutReader.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CalculateHsMetrics.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/CheckIlluminaDirectory.java
11
100.0
 src/main/java/org/broadinstitute/hellbender/utils/gene/RefFlatReader.java
12
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RrbsMetricsCollector.java
12
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/AbstractIlluminaPositionFileReader.java
13
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaDataProviderFactory.java
13
100.0
 src/main/java/org/broadinstitute/hellbender/utils/variant/DbSnpBitSetUtil.java
14
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CompareMetrics.java
14
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceStates.java
15
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaDataProvider.java
15
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/PerTilePerCycleFileUtil.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/MMapBackedIteratorFactory.java
16
100.0
 src/main/java/org/broadinstitute/hellbender/utils/gene/Gene.java
17
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileLocsParser.java
18
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ReadStructure.java
19
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/BclIndexReader.java
19
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 src/main/java/org/broadinstitute/hellbender/utils/illumina/IlluminaUtil.java
20
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/TileIndex.java
21
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/concordance/GenotypeConcordanceCounts.java
22
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/RenameSampleInVcf.java
26
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 src/main/java/org/broadinstitute/hellbender/tools/picard/fastq/ExtractSequences.java
26
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 src/main/java/org/broadinstitute/hellbender/utils/illumina/AdapterMarker.java
28
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/IlluminaBasecallsToFastq.java
28
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 src/main/java/org/broadinstitute/hellbender/tools/picard/interval/LiftOverIntervalList.java
29
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/FourChannelIntensityData.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/interval/ScatterIntervalsByNs.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ClusterData.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/IlluminaTextIterator.java
32
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 src/main/java/org/broadinstitute/hellbender/tools/picard/fastq/NormalizeFasta.java
35
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/IlluminaBasecallsToSam.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileBclFileUtil.java
36
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/MakeSitesOnlyVcf.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/HsMetricCollector.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileParser.java
40
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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/analysis/QualityScoreDistribution.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectMultipleMetrics.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/RnaSeqMetricsCollector.java
46
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/ExtractIlluminaBarcodes.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/readers/BclReader.java
48
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectTargetedMetrics.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/IlluminaBasecallsConverter.java
48
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/MergeVcfs.java
50
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/MultiTileBclParser.java
51
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectQualityYieldMetrics.java
71
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/MeanQualityByCycle.java
73
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/artifacts/ConvertSequencingArtifactToOxoG.java
75
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 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/parser/ClusterIntensityFileReader.java
88
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/MarkIlluminaAdapters.java
88
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/LiftoverVcf.java
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectBaseDistributionByCycle.java
121
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/CollectWgsMetrics.java
124
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectGcBiasMetrics.java
129
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 src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/GatherVcfs.java
153
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 src/main/java/org/broadinstitute/hellbender/tools/picard/interval/IntervalListTools.java
180
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/illumina/metrics/CollectHiSeqXPfFailMetrics.java
183
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/CollectOxoGMetrics.java
197
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 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/BamToBfq.java
279
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 src/main/java/org/broadinstitute/hellbender/tools/picard/analysis/directed/TargetMetricsCollector.java

Uncovered Existing Lines

Lines Coverage ∆ File
1
100.0
 src/main/java/org/broadinstitute/hellbender/tools/picard/sam/ReorderSam.java
Jobs
ID Job ID Ran Files Coverage
1 850.1 (TERM=dumb) 0
69.21
 Travis Job 850.1
Source Files on build 850
Detailed source file information is not available for this build.