Package picard.sam
Class SamComparisonMetric
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.sam.SamComparisonMetric
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
public class SamComparisonMetric
extends htsjdk.samtools.metrics.MetricBase
Metric for results of SamComparison. Used to store results in CompareSAMs.
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
Whether or not to consider the two input files equal.int
The number of primary records for which duplicate markings are different.Left file used in comparisonint
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.int
The number of primary records for which mappings match in files.int
The number of primary records which are found in right file but not found in left fileint
The number of primary records which are found in left file but not found in right fileRight file used in comparisonint
The number of primary records which are not mapped in either file.int
The number of primary records which are mapped in right file and found but not mapped in left fileint
The number of primary records which are mapped in left file and found but not mapped in right file -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionboolean
void
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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LEFT_FILE
Left file used in comparison -
RIGHT_FILE
Right file used in comparison -
MAPPINGS_MATCH
public int MAPPINGS_MATCHThe number of primary records for which mappings match in files. If running in strict alignment mode, this counts only records which are mapped in both files with the same alignment start positions and strands. If running with LENIENT_LOW_MQ_ALIGNMENT=true, then all records which are mapped in both files with mapping quality at most equal to LOW_MQ_THRESHOLD are counted as matching. If running with LENIENT_255_MQ_ALIGNMENT=true, all records which are mapped in both files with mapping quality 255 are counted as matches. -
MAPPINGS_DIFFER
public int MAPPINGS_DIFFERThe number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH. -
UNMAPPED_BOTH
public int UNMAPPED_BOTHThe number of primary records which are not mapped in either file. -
UNMAPPED_LEFT
public int UNMAPPED_LEFTThe number of primary records which are mapped in right file and found but not mapped in left file -
UNMAPPED_RIGHT
public int UNMAPPED_RIGHTThe number of primary records which are mapped in left file and found but not mapped in right file -
MISSING_LEFT
public int MISSING_LEFTThe number of primary records which are found in right file but not found in left file -
MISSING_RIGHT
public int MISSING_RIGHTThe number of primary records which are found in left file but not found in right file -
DUPLICATE_MARKINGS_DIFFER
public int DUPLICATE_MARKINGS_DIFFERThe number of primary records for which duplicate markings are different. If running in strict duplicate marking mode, any primary alignment which is marked as a duplicate in one file but not in the other will be counted. If running with LENIENT_DUP=true, we allow for swaps between duplicate and non-duplicate fragments in the same duplicate set to reduce the number of fragments with different duplicate marking. Note that this metric is counted on a per read basis, so a paired end fragment which differs in duplicate marking between the two files will increment this metric by 2. -
ARE_EQUAL
public boolean ARE_EQUALWhether or not to consider the two input files equal. The two input files are considered equal iff MAPPINGS_DIFFER == UNMAPPED_LEFT == UNMAPPED_RIGHT == MISSING_LEFT == MISSING_RIGHT == DUPLICATE_MARKINGS_DIFFER == 0 invalid input: '&'invalid input: '&' the headers have been compared to be equal. Note that the header comparison result can be dependent on whether the tool is run with LENIENT_HEADER true or false.
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Constructor Details
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SamComparisonMetric
public SamComparisonMetric()
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Method Details
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allVisitedAlignmentsEqual
public boolean allVisitedAlignmentsEqual() -
updateMetric
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