We have millions of paired-end alignments. They are stored in two sam files separately (but with consistent order). This is because we aligned the two read files (read_1.fastq, read_2.fastq) separately. Now we want to remove the duplicated pairs (those pairs with two identical alignments but in different alignment files, e.g., the alignment 1 in pair 1 is identical to the alignment 2 in 2, and the alignment 2 in pair 1 is identical to the alignment 1 in 2, are also treated as duplicates). Thanks!