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Id: 101438
Status: new
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Queue: Bio-SamTools

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Subject: CIGAR parsing error in Bio::DB::Sam
Date: Fri, 9 Jan 2015 18:42:22 -0600
To: <bug-Bio-SamTools [...]>
From: "Yun Heo" < [...]>
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Hello, I am using the Bio::DB::Sam module and it seems that the padded_alignment function of the module cannot recognize "X" and "=" in CIGAR strings. "M"s in CIGAR strings can also be represented using "X" and "=" to distinguish unmatched bases from matched ones. Could you check this problem? Thank you for your help in advance. Sincerely, Yun

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