@RG headers not being passed on to BAM

[santiagosnchez]

Hi,

I have sequencing data from different lanes/batches that I've merged into a single unaligned BAM. The headers in the merged unaligned bams look something like this:

@RG	ID:L001	SM:SAMPLEXXX	LB:L001	PL:Illumina
@RG	ID:L002	SM:SAMPLEXXX	LB:L002	PL:Illumina

But then when I run ngm-core using the --keep-tags flag these get ignored in the output file. However, the read group info in the reads is present (i.e., there are reads with their respective RG:Z:L001 and RG:Z:L002 tags).

I'm wondering if there is bug that is preventing the @RG headers to be passed on to the output file.

Thanks, Santiago