`--passthrough` with `--sam-append-comment`

[MikeWLloyd]

I found another place where --sam-append-comment is not writing correctly to the output. This time when using the --passthrough option.

The output is as follows:

A00739:517:HM2C7DSX2:4:1339:6551:28213	16	chr4	118734914	42	100M	*	0	0	CATTTGCCACCCACTCAGATATAAGGTTATCATGAGGCCTTGGCTGTGCGGGGCAATGGTAGTCTTTTGTGGACTATGGGGTGTCAGCTGTTCTCTGATC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UU
@A00739:517:HM2C7DSX2:4:1339:6551:28213 BC:Z:ATCATGCG+GTTGGTTG	ZA:Z:GTGT	ZB:Z:CCAGT	RX:Z:GTG-CCA	QX:Z:FFF FF:%0AGATCAGAGAACAGCTGACACCCCATAGTCCACAAAAGACTACCATTGCCCCGCACAGCCAAGGCCTCATGATAACCTTATATCTGAGTGGGTGGCAAATG%0A+%0AFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF%0A	BC:Z:ATCATGCG+GTTGGTTG	ZA:Z:GTGT	ZB:Z:CCAGT	RX:Z:GTG-CCA	QX:Z:FFF FF:

I think that the output should be something like this:

A00739:517:HM2C7DSX2:4:1339:6551:28213	16	chr4	118734914	42	100M	*	0	0	CATTTGCCACCCACTCAGATATAAGGTTATCATGAGGCCTTGGCTGTGCGGGGCAATGGTAGTCTTTTGTGGACTATGGGGTGTCAGCTGTTCTCTGATC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UU BC:Z:ATCATGCG+GTTGGTTG	ZA:Z:GTGT	ZB:Z:CCAGT	RX:Z:GTG-CCA	QX:Z:FFF FF:
@A00739:517:HM2C7DSX2:4:1339:6551:28213 BC:Z:ATCATGCG+GTTGGTTG	ZA:Z:GTGT	ZB:Z:CCAGT	RX:Z:GTG-CCA	QX:Z:FFF FF:%0AGATCAGAGAACAGCTGACACCCCATAGTCCACAAAAGACTACCATTGCCCCGCACAGCCAAGGCCTCATGATAACCTTATATCTGAGTGGGTGGCAAATG%0A+%0AFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF%0A