| 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> |
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
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