Package picard.sam.markduplicates

Class MarkDuplicatesForFlowArgumentCollection

java.lang.Object
picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
public class MarkDuplicatesForFlowArgumentCollection extends Object

  • Field Details

    • FLOW_MODE

      @Argument(doc="enable parameters and behavior specific to flow based reads.", optional=true) public boolean FLOW_MODE

    • FLOW_QUALITY_SUM_STRATEGY

      @Argument(doc="Use specific quality summing strategy for flow based reads. The strategy ensures that the same (and correct) quality value is used for all bases of the same homopolymer.", optional=true) public boolean FLOW_QUALITY_SUM_STRATEGY

    • USE_END_IN_UNPAIRED_READS

      @Argument(doc="Make the end location of single end read be significant when considering duplicates, in addition to the start location, which is always significant (i.e. require single-ended reads to start andend on the same position to be considered duplicate) (for this argument, \"read end\" means 3\' end).", optional=true) public boolean USE_END_IN_UNPAIRED_READS

    • USE_UNPAIRED_CLIPPED_END

      @Argument(doc="Use position of the clipping as the end position, when considering duplicates (or use the unclipped end position) (for this argument, \"read end\" means 3\' end).", optional=true) public boolean USE_UNPAIRED_CLIPPED_END

    • UNPAIRED_END_UNCERTAINTY

      @Argument(doc="Maximal difference of the read end position that counted as equal. Useful for flow based reads where the end position might vary due to sequencing errors. (for this argument, \"read end\" means 3\' end)", optional=true) public int UNPAIRED_END_UNCERTAINTY

    • FLOW_SKIP_FIRST_N_FLOWS

      @Argument(doc="Skip first N flows, starting from the read\'s start, when considering duplicates. Useful for flow based reads where sometimes there is noise in the first flows (for this argument, \"read start\" means 5\' end).", optional=true) public int FLOW_SKIP_FIRST_N_FLOWS

    • FLOW_Q_IS_KNOWN_END

      @Argument(doc="Treat position of read trimming based on quality as the known end (relevant for flow based reads). Default false - if the read is trimmed on quality its end is not defined and the read is duplicate of any read starting at the same place.", optional=true) public boolean FLOW_Q_IS_KNOWN_END

    • FLOW_EFFECTIVE_QUALITY_THRESHOLD

      @Argument(doc="Threshold for considering a quality value high enough to be included when calculating FLOW_QUALITY_SUM_STRATEGY calculation.", optional=true) public int FLOW_EFFECTIVE_QUALITY_THRESHOLD

  • Constructor Details

    • MarkDuplicatesForFlowArgumentCollection

      public MarkDuplicatesForFlowArgumentCollection()