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.
-
-
Field Summary
Fields Modifier and Type Field Description boolean
ARE_EQUAL
Whether or not to consider the two input files equal.int
DUPLICATE_MARKINGS_DIFFER
The number of primary records for which duplicate markings are different.String
LEFT_FILE
Left file used in comparisonint
MAPPINGS_DIFFER
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.int
MAPPINGS_MATCH
The number of primary records for which mappings match in files.int
MISSING_LEFT
The number of primary records which are found in right file but not found in left fileint
MISSING_RIGHT
The number of primary records which are found in left file but not found in right fileString
RIGHT_FILE
Right file used in comparisonint
UNMAPPED_BOTH
The number of primary records which are not mapped in either file.int
UNMAPPED_LEFT
The number of primary records which are mapped in right file and found but not mapped in left fileint
UNMAPPED_RIGHT
The number of primary records which are mapped in left file and found but not mapped in right file
-
Constructor Summary
Constructors Constructor Description SamComparisonMetric()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
allVisitedAlignmentsEqual()
void
updateMetric(SamComparison.AlignmentComparison comp)
-
-
-
Field Detail
-
LEFT_FILE
public String LEFT_FILE
Left file used in comparison
-
RIGHT_FILE
public String RIGHT_FILE
Right file used in comparison
-
MAPPINGS_MATCH
public int MAPPINGS_MATCH
The 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_DIFFER
The 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_BOTH
The number of primary records which are not mapped in either file.
-
UNMAPPED_LEFT
public int UNMAPPED_LEFT
The number of primary records which are mapped in right file and found but not mapped in left file
-
UNMAPPED_RIGHT
public int UNMAPPED_RIGHT
The number of primary records which are mapped in left file and found but not mapped in right file
-
MISSING_LEFT
public int MISSING_LEFT
The number of primary records which are found in right file but not found in left file
-
MISSING_RIGHT
public int MISSING_RIGHT
The number of primary records which are found in left file but not found in right file
-
DUPLICATE_MARKINGS_DIFFER
public int DUPLICATE_MARKINGS_DIFFER
The 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_EQUAL
Whether 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 && 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.
-
-
Method Detail
-
allVisitedAlignmentsEqual
public boolean allVisitedAlignmentsEqual()
-
updateMetric
public void updateMetric(SamComparison.AlignmentComparison comp)
-
-