The ADAPTER_* and BARCODE_* flags reflect whether the Subread in the ZMW, it will be available for all subreads in the ToolsĬonsuming the BAM should be aware that orientation information mayīe unavailable for subreads in a ZMW, but if is available for any Subreads from a ZMW, neither orientation flag should be set. Is up to tools producing the BAM to determine whether to useĪdapters or barcodes to reckon the orientation, but if passĭirections cannot be confidently and consistently assessed for the Per-ZMW convention, defining one element of the asymmetricīarcode/adapter pair as the “front” and the other as the “back”. Is considered a “forward” or “reverse” pass is determined by a Otherwise these flags must be left unset. Only if either the adapters or barcode design is asymmetric, Orientation of a subread (designated by one of the mutuallyĮxclusive FORWARD_PASS or REVERSE_PASS bits) can be reckoned Then any downstream application should only use CGCG in its analysis, andĮnum LocalContextFlags Flanking zeroes in kinetics arrays should be ignored for the respective strand.įor instance, when SEQ is AAACGCGTTT and fp:B:C,0,0,0,3,4,5,6,0,0,0,.These cases, empty lists will be passed for the respective record/orientationĪnd number of passes will be set to zero. Minor cases exist where a certain orientation may get filtered out entirelyįrom a ZMW, preventing valid values from being passed for that record.Passed as is from a representative subread. Have enough passes to generate HiFi reads. When CCS filtering is disabled, no averaging occurs with ZMWs that don’t.
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