Package picard.sam.util
Class SAMComparisonArgumentCollection
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- picard.sam.util.SAMComparisonArgumentCollection
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public class SAMComparisonArgumentCollection extends Object
Argument collection for SAM comparison
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Field Summary
Fields Modifier and Type Field Description boolean
LENIENT_DUP
boolean
LENIENT_HEADER
boolean
LENIENT_LOW_MQ_ALIGNMENT
boolean
LENIENT_UNKNOWN_MQ_ALIGNMENT
int
LOW_MQ_THRESHOLD
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Constructor Summary
Constructors Constructor Description SAMComparisonArgumentCollection()
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Field Detail
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LENIENT_HEADER
@Argument(doc="Perform lenient checking of header. In this mode, species, assembly, ur, m5, fields of sequence records, and pg fields in the header may all differ. Sequence record length must also be the same.") public boolean LENIENT_HEADER
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LENIENT_DUP
@Argument(doc="Perform lenient checking of duplicate marks. In this mode, will reduce the number of mismatches by allowing the choice of the representative read in each duplicate set to differ between the input files, as long as the duplicate sets agree.") public boolean LENIENT_DUP
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LENIENT_LOW_MQ_ALIGNMENT
@Argument(doc="Count reads which have mapping quality below LOW_MQ_THRESHOLD in both files but are mapped to different locations as matches. By default we count such reads as mismatching.") public boolean LENIENT_LOW_MQ_ALIGNMENT
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LENIENT_UNKNOWN_MQ_ALIGNMENT
@Argument(doc="Count reads for which no mapping quality is available (mapping quality value 255) in both files but are mapped to different locations as matches. By default we count such reads as mismatching.") public boolean LENIENT_UNKNOWN_MQ_ALIGNMENT
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LOW_MQ_THRESHOLD
@Argument(doc="When running in LENIENT_LOW_MQ_ALIGNMENT mode, reads which have mapping quality below this value will be counted as matches. if LENIENT_LOW_MQ_ALIGNMENT is false (default), then this argument has no effect.") public int LOW_MQ_THRESHOLD
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