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Output the sequence_alignment and germline_alignment fields in the AIRR format. Now TRUST4 outputs all the required fields in the AIRR format.
Output the AIRR file for the SMART-seq-like data.
Supporting barcodes at the molecular level
The secondary chain fields in the barcode_report file contain all types of chains. We also added the script "barcoderep-expand.py" to expand each barcode to represent those secondary chains for the case where each barcode contains multiple cells.