Package picard.analysis
Class AlignmentSummaryMetricsCollector
- java.lang.Object
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- picard.metrics.MultiLevelCollector<BEAN,HKEY,SAMRecordAndReference>
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- picard.metrics.SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,Integer>
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- picard.analysis.AlignmentSummaryMetricsCollector
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public class AlignmentSummaryMetricsCollector extends SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,Integer>
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
class
AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
Class that counts reads that match various conditions
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Field Summary
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Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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Constructor Summary
Constructors Constructor Description AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, List<String> adapterSequence, int maxInsertSize, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this recordprotected static int
get3PrimeSoftClippedBases(htsjdk.samtools.Cigar cigar, boolean negativeStrand)
returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.protected PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
makeChildCollector(String sample, String library, String readGroup)
Construct a PerUnitMetricCollector with the given arguments.-
Methods inherited from class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
makeArg
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Methods inherited from class picard.metrics.MultiLevelCollector
addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Constructor Detail
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AlignmentSummaryMetricsCollector
public AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, List<String> adapterSequence, int maxInsertSize, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
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Method Detail
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makeChildCollector
protected PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference> makeChildCollector(String sample, String library, String readGroup)
Description copied from class:MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.- Specified by:
makeChildCollector
in classMultiLevelCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
- Parameters:
sample
- If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collectorlibrary
- If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collectorreadGroup
- If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector- Returns:
- A PerUnitMetricCollector parameterized by the given arguments
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acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
Description copied from class:MultiLevelCollector
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record- Overrides:
acceptRecord
in classMultiLevelCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
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get3PrimeSoftClippedBases
protected static int get3PrimeSoftClippedBases(htsjdk.samtools.Cigar cigar, boolean negativeStrand)
returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.- Parameters:
cigar
- The input Cigar of the readnegativeStrand
- the negativeStrandFlag of the read- Returns:
- the amount of soft-clipping that the read has on its 3' end (the later read cycles)
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