to interval
sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
**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.
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**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