Test file Filtered

filtered.bam

This is a test file with chromosomes named after the alignment details to test (flag / quality):

@HD	VN:1.6	SO:coordinate
@SQ	SN:SUPPL	LN:404
@SQ	SN:DUPLI	LN:404
@SQ	SN:FAILQ	LN:404
@SQ	SN:NONPR	LN:404
@SQ	SN:VALID	LN:100
@SQ	SN:MAPQ0	LN:100
read1	1024	DUPLI	1	60	6M	*	0	0	CAGATA	IIIII9
read1	512	FAILQ	1	60	6M	*	0	0	CAGATA	IIIII9
read1	256	NONPR	100	60	6M	*	0	0	CAGATA	IIIII9
read1	2048	VALID	1	60	6M	*	0	0	CAGATA	IIIII9
read1	0	VALID	10	60	6M	*	0	0	CAGATA	IIIII9
read2	0	MAPQ0	10	0	6M	*	0	0	CACCAA	IIIII9

If running covtobed with minimum coverage 1:

./covtobed test/filtered.bam -m 1
DUPLI	0	6	1
FAILQ	0	6	1
NONPR	99	105	1
VALID	0	6	1
VALID	9	15	1
MAPQ0	9	15	1

If enabling the invalid alignments filter (new in 1.1.0):

./covtobed test/filtered.bam -m 1 -d
VALID	0	6	1
VALID	9	15	1