Specifically, the first half on each alignment record, due to a cut and paste error from the line above.
As quality values are stored one per byte, the line should be:
stats->checksum.quals += crc32(0L, qual, seq_len);
and not (seq_len+1)/2 as written.
If this is fixed, the change will need to be documented as quality checksums will change between samtools versions.
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