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*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])
*# A single-end record has the same key and a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])
* Mark both Paired-End Reads Duplicate if:
* Mark both Paired-End Reads Duplicate if:
# Another paired-end pair has the same set of keys and has a higher base quality sum.
# Another paired-end pair has the same set of keys and has a higher base quality sum (sum of all base qualities in the record above [[#Minimum Quality for Quality Calculations (--minQual)|<code>--minBaseQual</code>]])
This code assumes that at most 1000 bases are clipped at the start of a read.
This code assumes that at most 1000 bases are clipped at the start of a read.
