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Id: 54392
Status: new
Priority: 0/
Queue: Bio-SamTools

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Owner: Nobody in particular
Requestors: juan [...] ucsd.edu
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Subject: CQ tag bug
Date: Sun, 7 Feb 2010 12:17:44 -0800
To: bug-Bio-SamTools [...] rt.cpan.org, Lincoln Stein <lincoln.stein [...] gmail.com>
From: Juan Lorenzo Rodriguez Flores <juan [...] ucsd.edu>
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Dear Dr. Stein, I believe I have found a bug in the Alignment object. I am trying to extract the CQ (colorspace quality) string from an Bio::DB::Bam::Alignment object using the @values array. The CQ field is mangled and chopped into pieces. For example, the folowing code: my @tags=$aln->get_all_tags; foreach my $b (@tags) { print "$b\n"; } Prints out the following "tags": AS NH IH HI CS C Z8 89 4* ,7 47 ;7 57 ;9 8: 86 <> 5< 99 62 Show quoted text
>,
64 ;7 The first 5 are real tags, the rest are a chopped-up version of the quality string. The proper quality string is AS:i:1450 NH:i:1 IH:i:1 HI:i:1 CS:Z:t31200103321223210230002020132130130003000210112003 CQ:Z:858964*&,7;479;75576;968:>86?<><5<199162#>,864;;73 -- Juan Lorenzo Rodriguez-Flores, Ph.D. POSTAL: Moores UCSD Cancer Cente, # 0901 3855 Health Sciences Drive, La Jolla, CA 92093-0901 OFFICE: Moores 3rd Floor, Rm 3352 MAP: http://tinyurl.com/ltctyy BLOG: http://www.juansearch.com EMAIL: <juan@ucsd.edu>


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