to interval sam2interval.py --input_sam_file=$input1 $print_all > $out_file1 Yes No

**What it does** Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate. ----- **Example** Converting the following dataset:: r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * into Interval format will produce the following if *Print all?* is set to **Yes**:: ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA * ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA * ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1 ref 15 40 + r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC * ref 28 33 - r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0 ref 36 45 - r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT * Setting *Print all?* to **No** will generate the following:: ref 6 22 + r001 ref 8 19 + r002 ref 8 14 + r003 ref 15 40 + r004 ref 28 33 - r003 ref 36 45 - r001