Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-05-09

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All times shown according to UTC.

Time Nick Message
02:25 CIA-66 bioperl-live: Florent Angly master * r12b4405 / t/LocalDB/DBFasta.t : Removed a rogue temporary test file - http://git.io/o_YfPg
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14:12 driley Anyone here familiar with Bio::DB::Sam?
14:13 driley I'm trying to use the Bam seek function but it doesn't seem to actually change the position of my read pointer.
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16:38 pyrimidine driley: that interface is very geared towards gbrowse functionality (though I have used it for other things)
16:39 pyrimidine can you gist what you are doing?
16:39 pyrimidine (or nopaste)
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18:41 driley Hi pyrimidine, I'm need to basically index every 10000 lines in a bam file and then seek to the byte offset using that index.
18:46 driley pyrimidine, here is a cut/paste job of what I have. http://pastebin.com/uRtKqdUa
18:46 driley Basically the seek is having any effect on the subsequent iterator.
18:46 driley s/is/is not/
18:49 driley Had a typo in that last version: http://pastebin.com/C7tzWKS3
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21:15 pyrimidine driley: is it possible running the iterator is munging up the position?
21:16 pyrimidine oh, wait, no that shouldn't be it
21:18 pyrimidine I wonder if the higher-level (bioperl-specific) API is messing with the low-level XS stuff
21:20 pyrimidine e.g. when calling for an iterator, the position is reset regardless
21:24 pyrimidine driley_mac: yep, $self->reset_read is called prior to the iterator being returned
21:25 pyrimidine driley_mac: https://metacpan.org/source/LDS/Bio-S​amTools-1.33/lib/Bio/DB/Sam.pm#L1758
21:26 driley_mac thanks pyrimidine. Not sure what I can do about that.
21:26 pyrimidine looks like this is skipped if seqid is passed
21:26 pyrimidine *seq_id
21:28 pyrimidine my guess is, you may need to hack your own method in
21:47 driley_mac yeah, looks like it.
21:55 driley_mac It also appears as though seek doesn't put the pointer where I tell it
21:55 driley_mac If I do a tell right after the seek it is not the offset I pushed to seek.
22:02 driley_mac Also, if I try and do a read1 directly on the bam object I don't get anything valid
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