Figure 7
From: biobambam: tools for read pair collation based algorithms on BAM files
Pseudo code for pair and fragment list generation in duplicate marking algorithm. Pseudo code for list generation in duplicate marking algorithm. The input parameter C denotes a collating BAM file reader whose tryPair method fills the given pair and returns true if this operation was successful and false if no more reads could be obtained. The algorithm generates the lists L S and L P as described in the text. We assume that the tryPair method returns an unmapped read as the second component for orphan and single end reads.