Order mapped segements based on positions within the orginal read

Say I have a read with three mappings (chimeric read)

ReadName        Chrom        LeftPosition        RightPosition
READ1           1            10                  20
READ1           1            40                  50
READ1           3            20                  40

Is it possible for me to order the mappings as it was sequenced? Would the CIGAR string be key in this case?

Like looking at soft/hard clips and measuring the size of the alignments?

long-read

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written 9.1 years ago by QVINTVS_FABIVS_MAXIMVS

what is that format ? what is " mappings as it was sequenced? " ?

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written 9.1 years ago by Pierre Lindenbaum

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