samReadFilter: Filter a Sam object

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

Description

Apply a filter to a sam object, returing a new sam object with the sam header but only containing the reads for which the filter FUNC returns TRUE. Uses adply to apply this filter to each read alignment. Many of the parameters are just pass-through parameters for adply. These all begin with a "." to distinguish them from potential parameters to the function as they come after the ... in the function definition. No attempt is made to keep or delete both ends of a paired end read if one end passes and one end fails the filter.

Usage

samReadFilter(sam, FUNC, ..., .progress = "none", .inform = FALSE,
  .parallel = FALSE, .paropts = NULL, .id = NA)

Arguments

sam	A Sam object
FUNC	A function whose first parameter is a single read and that returns a single TRUE if that read should be kept when filtering the sam object, or FALSE if not. Should never return NULL or NA.
...	Other parameters to pass to FUNC.
.progress	Progress bar; see adply.
.inform	Extra error handling; see adply.
.parallel	Use the parallel package; see adply.
.paropts	Options if using the parallel package; see adply.
.id	Id column; see adply.

Details

NOTE: Does not add a @PG header line nor modify any PG:Z tag on any read.

Value

A sam object with only the reads that passed the filter FUNC.

See Also

Sam, readIsChimeric,

Examples

## Not run: 
sam <- Sam("someFile")
hivIntegrationSam <- samReadFilter( sam, "readIsOnRef", "^chrMT$" )

## End(Not run)

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