Subroutine Coverage

lib/Sanger/CGP/Vagrent/Annotators/AbstractAnnotator.pm
Criterion Covered Total %
subroutine 53 61 86.8
pod 4 8 50.0


line count pod subroutine
25 4 n/a BEGIN
27 4 n/a BEGIN
28 4 n/a BEGIN
29 4 n/a BEGIN
30 4 n/a BEGIN
31 4 n/a BEGIN
33 4 n/a BEGIN
35 4 n/a BEGIN
36 4 n/a BEGIN
38 4 n/a BEGIN
57 862 Yes new
67 0 No getConsensusSpliceOffsets
71 862 Yes getAnnotation
86 4 n/a BEGIN
89 639 Yes addMessage
94 14766 n/a _debug
103 1 Yes getMessages
109 862 n/a _clearMessages
113 862 n/a _assignBookmarks
121 4 n/a BEGIN
124 862 n/a _init
148 852 n/a _getmRNAPositions
429 441 n/a _buildProteinAnnotation
627 4 n/a BEGIN
629 4 n/a BEGIN
631 4 n/a BEGIN
634 441 n/a _buildCDSAnnotation
709 4 n/a BEGIN
711 4 n/a BEGIN
713 4 n/a BEGIN
715 4 n/a BEGIN
717 4 n/a BEGIN
720 152 n/a _buildUnknownCDSAnnotation
742 0 n/a _buildUnaffectedCDSAnnotation
763 377 n/a _buildUnknownProteinAnnotation
785 0 n/a _buildUnaffectedProteinAnnotation
806 3 n/a _buildRemovedProteinAnnotation
827 308 n/a _buildUnknownMRNAAnnotation
849 66 n/a _isOffsetAConsensusSpliceDistance
859 189 n/a _getConsesnsusSpliceBeforeBoundry
863 194 n/a _getConsesnsusSpliceAfterBoundry
867 692 n/a _isIntronicOffsetDistance
875 147 n/a _isWithin5KBOffsetDistance
883 0 No getUpDownStream5kbCutoff
887 142 n/a _isWithin2KBUpstreamOffsetDistance
895 0 No getUpStream2kbCutoff
899 121 n/a _isWithin500BPDownstreamOffsetDistance
907 0 No getDownStream500bpCutoff
912 371 n/a _coversStartCodon
948 371 n/a _coversStopCodon
983 862 n/a _getTranscriptSource
987 441 n/a _calculateCdsTranslationPadStrings
1020 441 n/a _canAnnotateToCDS
1088 441 n/a _canAnnotateToProtein
1124 487 n/a _revcompSeq
1134 26 n/a _sequenceStartsWithSequence
1152 26 n/a _calculateFrameShiftProteinChange
1202 14 n/a _calculateGenomicCdsPosition
1235 605 n/a _arrayHasString
1243 0 n/a _defaultTranscriptSort
1245 0 n/a __ANON__