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Convert SAM (version 1.0.2)
Do you want to retain original SAM fields? See example below.

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