readTests: 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. May return TRUE for only one end of a paired end read. These tests are suitable for use in a samReadFilter but can result in unpaired reads after application; pairedReads should probably be run after running any of these as filters.

areReadFlagsSet(read, flags)

areReadFlagsUnset(read, flags)

areReadFlags(read, flagVec)

readHasRef(read, ref)

readMateHasRef(read, ref)

`read`	The read to test.
`flags`	A character vector of one or more flag names to test against the flags set or unset for a read.
`flagVec`	A logical vector where the names are sam flags and the values indicate if that flag shoud be set (`TRUE`) or unset (`FLAG`). If the value of a flag does not matter, it should not be included. NA should not be used.
`ref`	Regular expression matched against the reference aligned to. Keeps a read if `ref` matches to the reference this read aligns to (`readHasRef()`, matching against `rname`) or the reference the mate of this read aligns to (`readMateHasRef()`, matching against `rnext`).

Returns TRUE if a read passes the test, FALSE otherwise. Different ends of the same template will return the same result.

areReadFlagsSet: Returns TRUE if all the specified flags are set for the read. Equivalent to allSetSamFlags(read$flag, flags)
areReadFlagsUnset: Returns TRUE if all the specified flags are set for the read. Equivalent to allUnsetSamFlags(read$flag, flags)
areReadFlags: Returns TRUE if all the flags that set in the flagVec are set for the read and all the flags that are unset in the flagVec are unset in the read. If all flags in the flagVec checked are set or all are unset, it is more efficient to use areReadFlagsSet or areReadFlagsUnset.
readHasRef: Returns TRUE if the read is aligned to a reference identified by the specified regular expressions (matched against the reads rname).
readMateHasRef: Returns TRUE if the read's mate (other paired end) is aligned to a reference identified by the specified regular expressions (matched against the reads rnext).

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

areReadFlagsUnset( aRead, "NOT_PRIMARY_ALIGNMENT" )
primaryReads <- samReadFilter( sam, "areReadFlagsUnset", "NOT_PRIMARY_ALIGNMENT" )

areReadFlagsSet( aRead, "NOT_PRIMARY_ALIGNMENT" )
secondaryReads <- samReadFilter( sam, "areReadFlagsSet", "NOT_PRIMARY_ALIGNMENT" )

goodAlignmentFlagVec <- c(
	"READ_PAIRED"           =  TRUE, "PROPER_PAIR"             =  TRUE,
   "READ_UNMAPPED"         = FALSE, "MATE_UNMAPPED"           = FALSE,
   "NOT_PRIMARY_ALIGNMENT" = FALSE, "READ_FAILS_VENDOR_QC"    = FALSE,
   "DUPLICATE_READ"        = FALSE, "SUPPLEMENTARY_ALIGNMENT" = FALSE
)
areReadFlags( aRead, goodAlignmentFlagVec )
goodReads <- samReadFilter( sam, "areReadFlags", goodAlignmentFlagVec )

## End(Not run)