countAllReads: Read statistics

Description Usage Arguments Value

View source: R/SamReads.R


Read statistics





A Sam or SamReads object to return read statistics for.

Returns the number of lines of reads in the Sam file. Does no filtering, so counts a multi-aligned read end once for each alignment and includes duplicates, unaligned reads, failed QC alignments, etc. Can filter and then re-apply to get any sub-scount desired. Dividing by 2 does not convert to paired end results as some ends may match more or less times than another.


Required for S3 object method implementation. Not currently used.


The total number of read records in the Sam file object.

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