pairedEndReadTests: Paired-end read tests
In jefferys/SamSeq: Work with aligned reads from a SAM file

Description Usage Arguments Value Functions Examples

Tests a read to see if its meets some criteria. Only tests that keep both or delete both reads when applied to each read end separately are paired-end read tests. These tests are suitable for use in a samReadFilter and will not result in unpaired reads after application.

pairIsAligned(read)

pairIsPrimary(read)

pairHasRef(read, ref)

pairIsChimeric(read, ref, altRef = NULL)

pairIsNotChimeric(read, ref)

`read`	The read to test.
`ref`	Regular expression matched against the reference that this end and/or the other end aligns to. Keeps a read if `ref` matches to either (`rname`) and/or (`rnext`).
`altRef`	Regular expression that matches the chromosome/reference name of whichever end `ref1` does not match.

Returns TRUE if a read passes the test, FALSE otherwise. Each read from the same template will return the same result.

pairIsAligned: selects paired end alignments when both ends are aligned. Relies on accuracy of READ_UNMAPPED and MATE_UNMAPPED flags and does not consider any other indicators. This will select non-primary alignments as well as primary alignments, if included in the sam file.
pairIsPrimary: selects paired end reads when both ends are aligned and are the primary alignment. Relies on accuracy of the READ_UNMAPPED, MATE_UNMAPPED, and NOT_PRIMARY_ALIGNMENT flags.
pairHasRef: Identifies paired end reads when one end is aligned to a selected reference or chromosome. Takes a regular expression and will return TRUE if either a reads rnext or rname (or both) matches it.
pairIsChimeric: Identifies paired end reads when one end is aligned to one reference or chromosome and the other end to a different one. Takes one or two regular expressions, and will return TRUE only if one read end matches the first expression and the other read end does not, or if altRef is specified if the other end matches that.
pairIsNotChimeric: Identifies paired end reads when both ends are aligned to the same reference or chromosome and the other end to a different one. Takes a regular expression, and will return TRUE only if both a reads rnext and rname match it.

## Not run: 
sam <- Sam("someFile")
aRead <- SamReads(sam)[1]

pairHasRef( aRead, "^chrX$|^chrY$" )
sexLinked <- samReadFilter( sam, "pairHasRef", "^chrX$|^chrY$" )

pairIsChimeric(aRead, "^chr..?$", "hiv|HIV")
hivIntegrationSam <- samReadFilter( sam, "pairIsChimeric", "^chr..?$", "hiv|HIV" )

pairIsNotChimeric(aRead, "hiv|HIV")
hivOnly <- samReadFilter( sam, "pairIsNotChimeric", "hiv|HIV" )


## End(Not run)