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Id: 123410
Status: resolved
Priority: 0/
Queue: Set-IntervalTree

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Owner: Nobody in particular
Requestors: muffato [...] ebi.ac.uk
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Subject: Missing output for fetch_window
Date: Fri, 27 Oct 2017 19:32:57 +0100
To: bug-Set-IntervalTree [...] rt.cpan.org
From: Matthieu Muffato <muffato [...] ebi.ac.uk>
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Hello, I am having issues with fetch_window. As I add more intervals/objects to the tree, some objects are not returned any more. It looks like the C++ code does not handle overlapping input overlaps, but it is not mentioned in the documentation of the module. I have attached a minimal test script. It adds elements one at a time to the tree, and queries a given interval (always the same) with fetch_window. It prints the returned array and the internal structure of the tree (even though I can't make sense of it). The list is supposed to remain the same or grow, reaching the elements 1, 2, 4, 6 and 7. But as soon as element 3 is added, the tree only returns the element 2. I think this is due to the end coordinate of element 3 being higher than the start coordinate of element 2. If I decrease the end coordinate to 6208751, none of the intervals overlap (but one is duplicated) and it works. However the documentation doesn't mention such a limitation. On the other hand, fetch doesn't seem to be affected by the overlap. It always correctly returns all the elements. I haven't looked into the C++ code, but could that mean that the structure is correct, but fetch_window makes too many assumptions about the intervals ? Bug replicated on: - v0.10, on perl v5.18.2 / Linux 3.13.0-132-generic (Ubuntu) - v0.11, on perl v5.24.1 / Linux 3.10.0-514.16.1.el7.x86_64 (RHEL7) I hope you can provide some guidance ! Thank you Best regards, Matthieu Muffato
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在2017-十月-27 14:37:57 星期五时,muffato@ebi.ac.uk写到: Show quoted text
> Hello, > > I am having issues with fetch_window. As I add more intervals/objects to > the tree, some objects are not returned any more. It looks like the C++ > code does not handle overlapping input overlaps, but it is not mentioned > in the documentation of the module. > > I have attached a minimal test script. It adds elements one at a time to > the tree, and queries a given interval (always the same) with > fetch_window. It prints the returned array and the internal structure of > the tree (even though I can't make sense of it). The list is supposed to > remain the same or grow, reaching the elements 1, 2, 4, 6 and 7. But as > soon as element 3 is added, the tree only returns the element 2. > > I think this is due to the end coordinate of element 3 being higher than > the start coordinate of element 2. If I decrease the end coordinate to > 6208751, none of the intervals overlap (but one is duplicated) and it > works. However the documentation doesn't mention such a limitation. > > On the other hand, fetch doesn't seem to be affected by the overlap. It > always correctly returns all the elements. I haven't looked into the C++ > code, but could that mean that the structure is correct, but > fetch_window makes too many assumptions about the intervals ? > > Bug replicated on: > - v0.10, on perl v5.18.2 / Linux 3.13.0-132-generic (Ubuntu) > - v0.11, on perl v5.24.1 / Linux 3.10.0-514.16.1.el7.x86_64 (RHEL7) > > I hope you can provide some guidance ! > > Thank you > > Best regards, > Matthieu Muffato
This should be fixed now in release 0.12.
Subject: Re: [rt.cpan.org #123410] Missing output for fetch_window
Date: Tue, 19 Jun 2018 14:15:45 +0100
To: bug-Set-IntervalTree [...] rt.cpan.org
From: Matthieu Muffato <muffato [...] ebi.ac.uk>
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It seems to be working now, yes. Thank you for your work ! Matthieu On 10/06/18 06:21, Stephan Loyd via RT wrote: Show quoted text
> <URL: https://rt.cpan.org/Ticket/Display.html?id=123410 > > > 在2017-十月-27 14:37:57 星期五时,muffato@ebi.ac.uk写到:
>> Hello, >> >> I am having issues with fetch_window. As I add more intervals/objects to >> the tree, some objects are not returned any more. It looks like the C++ >> code does not handle overlapping input overlaps, but it is not mentioned >> in the documentation of the module. >> >> I have attached a minimal test script. It adds elements one at a time to >> the tree, and queries a given interval (always the same) with >> fetch_window. It prints the returned array and the internal structure of >> the tree (even though I can't make sense of it). The list is supposed to >> remain the same or grow, reaching the elements 1, 2, 4, 6 and 7. But as >> soon as element 3 is added, the tree only returns the element 2. >> >> I think this is due to the end coordinate of element 3 being higher than >> the start coordinate of element 2. If I decrease the end coordinate to >> 6208751, none of the intervals overlap (but one is duplicated) and it >> works. However the documentation doesn't mention such a limitation. >> >> On the other hand, fetch doesn't seem to be affected by the overlap. It >> always correctly returns all the elements. I haven't looked into the C++ >> code, but could that mean that the structure is correct, but >> fetch_window makes too many assumptions about the intervals ? >> >> Bug replicated on: >> - v0.10, on perl v5.18.2 / Linux 3.13.0-132-generic (Ubuntu) >> - v0.11, on perl v5.24.1 / Linux 3.10.0-514.16.1.el7.x86_64 (RHEL7) >> >> I hope you can provide some guidance ! >> >> Thank you >> >> Best regards, >> Matthieu Muffato
> > > This should be fixed now in release 0.12. >
-- Matthieu Muffato, Ph.D. Ensembl Compara and TreeFam Project Leader European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus, Hinxton Cambridge, CB10 1SD, United Kingdom Room A3-145 Phone + 44 (0) 1223 49 4631 Fax + 44 (0) 1223 49 4468


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