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This queue is for tickets about the Bio-SamTools CPAN distribution.

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The Basics
Id: 52363
Status: new
Priority: 0/
Queue: Bio-SamTools

Owner: Nobody in particular
Requestors: madhu.donepudi [...]

Bug Information
Severity: (no value)
Broken in: 1.07
Fixed in: (no value)

Subject: Inconsistent return values in Bio::DB::Sam->features method
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The Bio::DB::Sam->features call returns a list of AlignWrapper objects, but if used to create an Iterator, the Iterator returns Alignment objects. See the following; my $sam = Bio::DB::Sam->new(-bam =>"/path/to/my.bam"); foreach my $a( $sam->features() ){ # $a is a Bio::DB::Bam::AlignWrapper } my $iterator = $sam->features(-iterator=>1); while (my $a = $iterator->next_seq){ # $a is a Bio::DB::Bam::Alignment }

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