getFileLineCount: Manange Line and Read Counts for Large Files

Description Usage Arguments Details Note

Description

Routines to keep track of the number of lines and/or short reads in large files, typically NextGen sequencing data

Usage

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getFileLineCount(f, sampleID = "", verbose = TRUE, mode = "full", 
		 what = c("lineCount", "readCount"))

quickFileLineCountLookup(f, sampleID = "", what = c("lineCount", "readCount"))
quickFileLineCountRecord(f, sampleID = "", lineCount, readCount = lineCount)

Arguments

f

the name of one file, that we want to find or record line/read count information about

sampleID

an optional SampleID, to specify which FileLineCount file to use

mode

character string, denotes if we need the actual exact number of lines, or just enough to confirm that the file is not empty. See details.

what

the type of count, either actual lines of text, or the number of reads/sequences

lineCount

the number of actual lines of text

readCount

the number of actual reads/sequences

Details

These routine help manage the very large files typical of NextGen data. They help facilitate file buffering, and are helpful for generating summary statistics about alignment results.

The 'get' and 'lookup' routines return one numeric value, giving the size of the file in 'what' units. When 'mode' is not 'full', it returns the count from the first buffer. For files that are not found, or other errors, zero is returned. The 'record' routine updates the FileLineCount file to the true counts, and is typically called after a computationally intense step, to let other later functions know how big the various files are without having to explicitly count records.

Note

The counts are stored in files called '.FileLineCount.<SampleID>'. If abnormal or unexpected behaviors occur with a particular sample, try deleting its FileLineCount file; a new one will get re-created over time.


robertdouglasmorrison/DuffyTools documentation built on Dec. 7, 2018, 8:02 a.m.