Coverage Summary

Module Bio-Roary
Version 3.10.1
Database: /root/.cpan/build/Bio-Roary-3.10.1-0/cover_db
Report date: 2017-09-07 16:19:55
Perl version: v5.26.0
OS: linux
Thresholds: < 75% < 90% < 100% = 100%

Restrict to regex:

file stmt bran cond sub pod time total
Total 78.5 52.5 36.9 87.4 0.0 100.0 72.9
lib/Bio/Roary.pm 79.0 16.6 n/a 100.0 0.0 0.1 75.2
lib/Bio/Roary/AccessoryBinaryFasta.pm 81.1 75.0 83.3 91.6 0.0 1.0 81.2
lib/Bio/Roary/AccessoryClustering.pm 33.3 0.0 n/a 71.4 n/a 1.0 35.7
lib/Bio/Roary/AnalyseGroups.pm 93.2 60.0 n/a 88.8 0.0 5.8 87.3
lib/Bio/Roary/AnnotateGroups.pm 91.8 70.4 55.5 90.0 0.0 4.3 86.0
lib/Bio/Roary/AssemblyStatistics.pm 93.0 69.4 58.3 92.8 0.0 1.2 84.9
lib/Bio/Roary/BedFromGFFRole.pm 93.5 56.2 n/a 100.0 n/a 0.2 82.6
lib/Bio/Roary/ChunkFastaFile.pm 100.0 100.0 n/a 100.0 n/a 2.1 100.0
lib/Bio/Roary/ClustersRole.pm 100.0 100.0 n/a 100.0 n/a 0.0 100.0
lib/Bio/Roary/CombinedProteome.pm 100.0 100.0 n/a 100.0 0.0 1.9 92.8
lib/Bio/Roary/CommandLine/Common.pm 80.0 n/a n/a 71.4 0.0 0.4 75.0
lib/Bio/Roary/CommandLine/CreatePanGenome.pm 90.0 n/a n/a 85.7 0.0 0.0 85.7
lib/Bio/Roary/CommandLine/ExtractProteomeFromGff.pm 84.0 62.5 n/a 100.0 0.0 1.9 76.4
lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm 41.5 0.0 0.0 75.0 0.0 1.7 34.6
lib/Bio/Roary/CommandLine/ParallelAllAgainstAllBlastp.pm 81.6 76.9 n/a 100.0 0.0 1.4 79.5
lib/Bio/Roary/CommandLine/QueryRoary.pm 92.9 85.0 61.1 100.0 0.0 1.1 86.3
lib/Bio/Roary/CommandLine/Roary.pm 64.0 41.1 16.6 88.8 0.0 0.0 54.4
lib/Bio/Roary/CommandLine/RoaryCoreAlignment.pm 91.9 75.0 66.6 100.0 0.0 1.0 84.5
lib/Bio/Roary/CommandLine/RoaryPostAnalysis.pm 27.2 0.0 0.0 57.1 0.0 1.1 19.3
lib/Bio/Roary/CommandLine/RoaryReorderSpreadsheet.pm 93.9 81.8 70.8 100.0 0.0 0.9 82.0
lib/Bio/Roary/CommandLine/TransferAnnotationToGroups.pm 80.4 62.5 33.3 100.0 0.0 0.9 72.8
lib/Bio/Roary/ContigsToGeneIDsFromGFF.pm 65.1 27.2 55.5 85.7 n/a 2.1 57.6
lib/Bio/Roary/Exceptions.pm 100.0 n/a n/a 100.0 n/a 0.0 100.0
lib/Bio/Roary/External/Blastp.pm 100.0 n/a n/a 100.0 0.0 0.2 94.1
lib/Bio/Roary/External/Cdhit.pm 93.5 83.3 n/a 85.7 0.0 0.9 86.9
lib/Bio/Roary/External/CheckTools.pm 77.0 50.0 50.0 100.0 0.0 1.0 67.2
lib/Bio/Roary/External/Fasttree.pm 23.0 0.0 0.0 40.0 0.0 0.0 19.5
lib/Bio/Roary/External/GeneAlignmentFromNucleotides.pm 11.7 0.0 0.0 28.5 0.0 0.0 9.6
lib/Bio/Roary/External/IterativeCdhit.pm 21.4 0.0 n/a 33.3 0.0 0.0 19.5
lib/Bio/Roary/External/Mafft.pm 95.6 50.0 n/a 100.0 0.0 0.0 90.6
lib/Bio/Roary/External/Makeblastdb.pm 100.0 n/a n/a 100.0 0.0 2.0 96.7
lib/Bio/Roary/External/Mcl.pm 85.7 66.6 n/a 100.0 0.0 1.0 83.6
lib/Bio/Roary/External/PostAnalysis.pm 13.0 0.0 0.0 27.2 0.0 0.0 9.4
lib/Bio/Roary/External/Prank.pm 95.6 50.0 n/a 100.0 0.0 0.1 90.6
lib/Bio/Roary/ExtractCoreGenesFromSpreadsheet.pm 100.0 90.0 50.0 100.0 n/a 1.2 93.8
lib/Bio/Roary/ExtractProteomeFromGFF.pm 52.1 25.0 n/a 70.8 n/a 1.3 52.2
lib/Bio/Roary/ExtractProteomeFromGFFs.pm 84.4 50.0 n/a 90.0 n/a 1.1 84.2
lib/Bio/Roary/FilterFullClusters.pm 94.5 70.0 50.0 100.0 0.0 1.0 86.7
lib/Bio/Roary/FilterUnknownsFromFasta.pm 100.0 100.0 n/a 100.0 n/a 0.3 100.0
lib/Bio/Roary/GeneNamesFromGFF.pm 97.3 66.6 n/a 100.0 n/a 4.8 88.5
lib/Bio/Roary/GroupLabels.pm 100.0 50.0 n/a 100.0 0.0 0.9 90.0
lib/Bio/Roary/GroupStatistics.pm 95.8 77.7 66.6 100.0 0.0 2.1 92.2
lib/Bio/Roary/InflateClusters.pm 82.0 42.8 n/a 100.0 0.0 0.9 75.3
lib/Bio/Roary/JobRunner/Local.pm 77.7 50.0 n/a 71.4 0.0 23.2 71.0
lib/Bio/Roary/JobRunner/Role.pm 96.5 66.6 n/a 100.0 n/a 1.7 92.6
lib/Bio/Roary/LookupGeneFiles.pm 94.1 50.0 n/a 100.0 n/a 0.0 90.9
lib/Bio/Roary/MergeMultifastaAlignments.pm 100.0 75.0 n/a 100.0 0.0 0.0 94.8
lib/Bio/Roary/OrderGenes.pm 92.6 77.7 41.6 94.7 n/a 1.6 89.1
lib/Bio/Roary/Output/BlastIdentityFrequency.pm 46.1 0.0 n/a 57.1 0.0 0.0 42.1
lib/Bio/Roary/Output/CoreGeneAlignmentCoordinatesEMBL.pm 100.0 50.0 n/a 100.0 0.0 1.1 96.0
lib/Bio/Roary/Output/DifferenceBetweenSets.pm 100.0 n/a n/a 100.0 0.0 1.1 92.1
lib/Bio/Roary/Output/EMBLHeaderCommon.pm 94.7 50.0 n/a 100.0 n/a 0.0 92.0
lib/Bio/Roary/Output/EmblGroups.pm 24.3 11.1 0.0 47.3 0.0 1.0 21.1
lib/Bio/Roary/Output/GroupMultifasta.pm 97.2 66.6 n/a 100.0 0.0 0.4 92.3
lib/Bio/Roary/Output/GroupsMultifastaNucleotide.pm 65.7 27.7 0.0 86.9 0.0 0.0 62.7
lib/Bio/Roary/Output/GroupsMultifastaProtein.pm 100.0 n/a n/a 100.0 0.0 1.2 97.8
lib/Bio/Roary/Output/GroupsMultifastas.pm 100.0 50.0 n/a 100.0 0.0 0.9 93.5
lib/Bio/Roary/Output/GroupsMultifastasNucleotide.pm 92.3 50.0 n/a 100.0 0.0 0.0 90.2
lib/Bio/Roary/Output/NumberOfGroups.pm 100.0 100.0 n/a 100.0 0.0 0.0 98.9
lib/Bio/Roary/Output/QueryGroups.pm 100.0 70.0 n/a 100.0 0.0 1.1 94.0
lib/Bio/Roary/ParallelAllAgainstAllBlast.pm 98.7 50.0 n/a 100.0 0.0 0.9 93.4
lib/Bio/Roary/ParseGFFAnnotationRole.pm 80.0 n/a n/a 75.0 n/a 0.4 78.5
lib/Bio/Roary/PostAnalysis.pm 35.5 0.0 0.0 51.4 0.0 0.0 33.9
lib/Bio/Roary/PrepareInputFiles.pm 92.7 62.5 n/a 94.1 0.0 1.2 88.5
lib/Bio/Roary/PresenceAbsenceMatrix.pm 100.0 66.6 66.6 100.0 0.0 0.1 93.6
lib/Bio/Roary/QC/Report.pm 39.8 0.0 0.0 59.0 0.0 0.9 37.5
lib/Bio/Roary/ReformatInputGFFs.pm 93.0 63.1 100.0 100.0 0.0 1.4 87.1
lib/Bio/Roary/ReorderSpreadsheet.pm 90.1 50.0 n/a 100.0 0.0 1.1 88.1
lib/Bio/Roary/SampleOrder.pm 100.0 100.0 n/a 100.0 n/a 1.8 100.0
lib/Bio/Roary/SequenceLengths.pm 100.0 n/a n/a 100.0 n/a 2.0 100.0
lib/Bio/Roary/SortFasta.pm 100.0 95.8 88.8 100.0 0.0 3.2 96.3
lib/Bio/Roary/SplitGroups.pm 93.3 94.1 100.0 95.8 0.0 1.2 93.4
lib/Bio/Roary/SpreadsheetRole.pm 90.9 50.0 n/a 87.5 0.0 0.0 84.8
lib/Bio/Roary/UniqueGenesPerSample.pm 97.2 58.3 n/a 100.0 0.0 0.9 87.2