Check physical coverage

Check physical coverage

The physical coverage can be evaluated when analyzing paired-end or mate paired libraries.

In the repository a simulated mate paired library has been aligned and the sorted BAM file is available in test/mp.bam.

Command:

covtobed --physical-coverage --min 10 test/mp.bam

Output:

NC_001416.1	40	51	10
NC_001416.1	51	52	11
NC_001416.1	52	56	12
NC_001416.1	56	59	13
NC_001416.1	59	62	14
NC_001416.1	62	63	15
NC_001416.1	63	64	16
NC_001416.1	64	66	17
NC_001416.1	66	73	18
NC_001416.1	73	78	19