Description Usage Arguments Value See Also Examples
'alnIndex' returns the alignment index from a PacBioCmpH5 object, including information about ID, alnGroupPath, movieName, refName, tStart, tEnd, alignedStrand, holeNumber, setNumber, strobeNumber, moleculeID, rStart, rEnd, mapQV, nMatches, nMisMatches, nInsertions, ndeletions, offsetBegin, offsetEnd, nBackRead and nOverlap.
1 | alnIndex(cmpH5)
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cmpH5 |
An object of class PacBioCmpH5 |
'alnIndex' returns a data.frame where each row represents an alignment, and each column represents unique information about the alignment. 'alnGroup' returns a data.frame where each row is a unique Path. See description.
1 2 3 4 5 6 7 8 | require(pbh5)
cmpH5 <- PacBioCmpH5(system.file("h5_files", "aligned_reads.cmp.h5",
package = "pbh5"))
alignments <- alnIndex(cmpH5)
class(alignments)
head(alignments)
alignGroup <-alnGroup(cmpH5)
head(alignGroup)
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