BamUtil: writeRegion
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Overview of the writeRegion
function of bamUtil
The writeRegion
option on the bamUtil executable uses an indexed BAM file to only write the alignments that:
- fall within the region specified
- region as defined by
refID
orrefName
andstart
and/orend
- region as defined in the
bed
file - overlapping or fully within if
--withinReg
is specified
- region as defined by
- have a specific read name (if specified)
Parameters
Required Parameters: --in : the BAM file to be read --out : the SAM/BAM file to write to Optional Parameters: --bamIndex : the path/name of the bam index file (if not specified, uses the --in value + ".bai") --refName : the BAM reference Name to read Either this or refID can be specified. Defaults to all references. --refID : the BAM reference ID to read. Either this or refName can be specified. Defaults to all references. Specify -1 for unmapped --start : inclusive 0-based start position. Defaults to -1: meaning from the start of the reference. Only applicable if refName/refID is set. --end : exclusive 0-based end position. Defaults to -1: meaning til the end of the reference. Only applicable if refName/refID is set. --bed : use the specified bed file for regions. --withinReg : only print reads fully enclosed within the region. --readName : only print reads with this read name. --params : print the parameter settings --noeof : do not expect an EOF block on a bam file.
Usage
./bam writeRegion --in <inputFilename> --out <outputFilename> [--bamIndex <bamIndexFile>] [--refName <reference Name> | --refID <reference ID>] [--start <0-based start pos>] [--end <0-based end psoition>] [--bed <bed filename>] [--withinRegion] [--readName <readName>] [--params] [--noeof]
Return Value
- 0: all records are successfully read and written.
- non-0: at least one record was not successfully read or written.
Example Output
Wrote t.sam with 2 records.