BamUtil: findCigars

Overview of the findCigars function of bamUtil

The findCigars option on the bamUtil executable outputs just the reads that contain any of the specified CIGAR operations.

Parameters

	Required Parameters:
		--in         : the SAM/BAM file to be read
		--out        : the SAM/BAM file to be written
	Optional Parameters:
		--cinsert     : output reads that contain insertions ('I').
		--cdel        : output reads that contain deletions ('D').
		--cpad        : output reads that contain pads ('P').
		--cskip       : output reads that contain skips ('N').
		--chardClip   : output reads that contain hard clips ('H').
		--csoftClip   : output reads that contain soft clips ('S').
		--nonM       : output reads that contain any non match/mismatch (anything other than 'M', '=', 'X')
		--noeof      : do not expect an EOF block on a bam file.
		--params     : print the parameter settings

Usage

./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]

Return Value

Returns the SamStatus for the reads/writes.

Example Output

Number of records read = 10
Number of records written = 1