some complex tag values will still break output BAM header, even after hotfix 2.3.4

[byb121]

for example:
in the input BAM:

@RG	ID:2977244	PL:HiSeq	PU:13$'"617_6	LB:EM-2_rnas"|||eq 1!100$5739_52200	PI:125	MI:494	DS:s h`o r\\\	PG:2977244	SM:EM-2	CN:SANGER

star_mapping.pl will escape the tags correctly and pass them to star, so the command line is like this:

 #!/bin/bash
set -eux
 /opt/wtsi-cgp/bin/STAR  [...other_star_options] --outSAMattrRGline "ID:2977244" "PL:HiSeq" "PU:13\$'\"617_6" "LB:EM-2_rnas\"|||eq 1\!100\$5739_52200" "PI:125" "MI:494" "DS:s h\`o r\\\\\\" "PG:2977244" "SM:test_bad_header" "CN:SANGER"

However, the output BAM has header:

@RG	ID:2977244	PL:HiSeq	PU:13$'"617_6	LB:EM-2_rnas	|||eq	1\!100$5739_52200"	PI:125	MI:494	DS:s h`o r\\\	PG:2977244	SM:test_bad_header	CN:SANGER

Note that the LB tag has been split into three tags.

It looks like a bug in Star.

[byb121]

I'll test if the latest version of Star outputs the same header.

[byb121]

latest version of STAR:2.7.2a failed to interpret the RG line correctly as well, as in the issue I raised here: alexdobin/STAR#725

We'll have to wait for fixes in STAR.