AssignReadGroupByBarcode 'UNEXPECTED ERROR: 1'

This error is solved in versions > 1.0.0

In version 1.0.0 or lower, when a barcode file with more than one barcode is provided and the barcodes are not encoded in the BC tag separated by hyphens as recommended in the SAM specifications. There are several reported cases:
  • Barcodes encoded in two different tags. For example, BAM files obtained with illumina2bam use to have dual-indexed datasets with the first barcode in the BC tag and the second in the B2 tag. This could be fixed by using the following options: --rawBarcodeSequenceTags BC --rawBarcodeSequenceTags B2. Data from other sources may require a different values for this argument.
  • Barcode encoded in the BC tag but separated with a custom character. In this case, we recommend to reformat your data with awk or sed. We also have implemented an advance solution for laboratories where the data is always encoded with a custom separator, and it should not be modified (for more information, see ReadTools Java Properties).

Exception in thread "main" java.lang.NoClassDefFoundError: org/xerial/snappy/LoadSnappy

This error is solved in versions > 1.0.0

If your command fail with this error, the solution is to re-run it using java -Dsnappy.disable=true -jar ReadTools.jar.