Metadamage getdamage for paired-end reads with bwa mem

[RAHenriksen]

When running metadamage getdamage on paired-end reads obtained from bwa-mem the program doesn't output information to the bdamage.gz file.

./metadamage getdamage -l 15 -p 7 -o test -r 0 XXpe.bam
./metadamage refName: (null) minLength: 15 printLength: 7 runmode: 0 outname: test nthreads: 4
skipping: K00171:751:HW5LWBBXX:8:2101:17858:19390 is paired (can be considered using the -paired flag, this msg is printed 2 times more
skipping: K00171:751:HW5LWBBXX:8:2228:20050:23399 is paired (can be considered using the -paired flag, this msg is printed 1 times more
skipping: K00171:751:HW5LWBBXX:8:2101:17858:19390 is paired (can be considered using the -paired flag, this msg is printed 0 times more
-> Will dump: 'test.res.gz' this contains damage patterns for: 0 items
-> Setting threads to: 4
-> Will dump: 'test.bdamage.gz' this contains damage patterns for: 0 items
-> Setting threads to: 4

The errorr message is only shown for the first three reads in the file with one being the read-pair "K00171:751:HW5LWBBXX:8:2101:17858:19390" and another being " K00171:751:HW5LWBBXX:8:2228:20050:23399"

When trying again with the -paired flag, it still fails.