BAM_Files: Utilities for Manipulating BAM Files.

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Utilities for Manipulating BAM Files.

Description

A variety of functions for operating on BAM and SAM files, as may be needed by various DuffyNGS pipeline tools or SAMTOOLS utilities.

Usage

BAM.sort(file, what = c("position", "readID"), index = TRUE, memory = 2.147e+09, threads = 2, verbose = TRUE)
BAM.index(file, verbose = TRUE)
BAM.verifySorted(file, index = TRUE, threads = 2, verbose = TRUE)
BAM.merge(files, newfile, index = TRUE, verbose = TRUE)
BAM.indexFASTA(file, verbose = TRUE)
BAM.fieldTable(file, field, chunkSize = 100000, maxReads = NULL, verbose = TRUE)
cleanupBAMfiles( path = "results")
SAM2BAM(file, verbose = TRUE, delete.SAM = TRUE)

Arguments

file, files	Character string full pathname of one existing BAM file. Or a character vector of 2+ BAM files.
what	Character vector of named fields in the BAM file to do the sorting on.
index	Logical, should the sort BAM file have its sort index (.bai) file created as well.
memory	Size of local memory in bytes for sort scratch space.
threads	Allows use of multithreading to improve sort time performance.
newfile	Filename for the newly created BAM file.
field	Character string of a single field in the BAM file, to be the value that gets inspected.
chunkSize	Numeric buffer size, number of BAM file alignments to read into memory at a time.
maxReads	Numeric, maximum number of BAM file alignments to inspect.
path	Character string of a top level results folder, that contains various alignment pipeline result subfolders.

Details

These utility functions are designed to do typical error checking about file existence, etc., so higher level pipeline tools don't have to. Most are just simple wrappers around system calls to SAMTOOLS functions.

Value

For BAM.sort, when successful, the filename of the created sorted BAM file.

For BAM.index, when successful, the filename of the created BAM index file.

For BAM.verifySorted, when successful, the filename of the BAM file.

For BAM.merge, when successful, the filename of the new merged BAM file.

For BAM.indexFASTA, when successful, the filename of the created FASTA index file.

For BAM.fieldTable, a data frame that tallies the counts and percentage for each value observed for that field in the BAM file.

For cleanupBAMfiles, a brief summary of file counts and bytes of disk space deleted.

For SAM2BAM, when successful, the filename of the created BAM file.

Note

There are many other low level functions for operating on the contents of BAM files, either one alignment at a time or in buffered chunks of alignments. For a brief introduction, see bamReader.

Author(s)

Bob Morrison

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.