testSamFlags: Test if sam flags are set or unset.

In jefferys/SamSeq: Work with aligned reads from a SAM file

Description

Logically compares one or more sam flags against an encoded sam value.

Usage

allSetSamFlags(val, flags)

allUnsetSamFlags(val, flags)

anySetSamFlags(val, flags)

anyUnsetSamFlags(val, flags)

matchSamFlags(val, flagVec)

Arguments

val	The encoded sam flag value to check, as a single integer value
flags	The flags to test, as a character vector.
flagVec	A logical vector where the names are sam flags and the values indicate if that flag shoud be set (TRUE) or unset (FALSE). If the value of a flag does not matter, it should not be included. NA should not be used.

Details

Note: allSetSamFlags == ! anyUnsetSamFlags, and allUnsetSamFlags == ! anySetSamFlags

Value

A single TRUE or FALSE value

Functions

• allSetSamFlags: TRUE only if all specified flags are set, FALSE if any specified flag is unset. The status of unspecified flags does not matter.

• allUnsetSamFlags: TRUE only if all specified flags are unset, FALSE if any specified flags is set. The status of unspecified flags does not matter.

• anySetSamFlags: TRUE if any specified flag is set, FALSE only if all specified flags are unset. The status of unspecified flags does not matter.

• anyUnsetSamFlags: TRUE if any specified flag is unset, FALSE only if all specified flags are set. The status of unspecified flags does not matter.

• matchSamFlags: TRUE if all flags specified as TRUE are set and all flags specified as FALSE are unset. The status of unspecified flags does not matter.

Examples

# READ_PAIRED = 1, PROPER_PAIR = 2
# All TRUE
allSetSamFlags( 1 + 2, c( "READ_PAIRED", "PROPER_PAIR" ))
anySetSamFlags( 1 + 2, c( "READ_PAIRED", "PROPER_PAIR" ))
anySetSamFlags( 1 + 2, "READ_PAIRED")
allUnsetSamFlags( 4, c( "READ_PAIRED", "PROPER_PAIR" ))
anyUnsetSamFlags( 1, "PROPER_PAIR" )
anyUnsetSamFlags( 1, c( "READ_PAIRED", "PROPER_PAIR" ))

# All FALSE
allSetSamFlags( 1, "PROPER_PAIR" )
allSetSamFlags( 1, c( "READ_PAIRED", "PROPER_PAIR" ))
anySetSamFlags( 4, c( "READ_PAIRED", "PROPER_PAIR" ))
allUnsetSamFlags( 1 + 2, c( "READ_PAIRED", "PROPER_PAIR" ))
allUnsetSamFlags( 1 + 2, "READ_PAIRED" )
anyUnsetSamFlags( 1 + 2, c( "READ_PAIRED", "PROPER_PAIR" ))

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
)
matchSamFlags( 1+2, goodAlignmentFlagVec )    # TRUE
matchSamFlags( 1+2+4, goodAlignmentFlagVec )  # FALSE
matchSamFlags( 1, goodAlignmentFlagVec )  # FALSE

jefferys/SamSeq documentation built on Oct. 25, 2019, 8:11 a.m.