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fulcrumgenomics / fgbio

Tools for working with genomic and high throughput sequencing data.
http://fulcrumgenomics.github.io/fgbio/
MIT License
309 stars 67 forks source link

Make ZipperBams hanlde program name collisions #1006

Open bwlang opened 1 month ago

bwlang commented 1 month ago

I had to add --no-PG to my ubam generation code to avoid name collisions. to reproduce create a ubam with samtools cat and samtool collate. then use samtools collate to product the aligned bam.

bwlang commented 1 month ago

here is the specific error: java.lang.IllegalArgumentException: Program record with group id samtools already exists in SAMFileHeader!