Bugs
From BioPerl
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Bug submission
Please submit bugs or enhancement requests to the BioPerl Bugzilla tracking system. We really do want you to submit bugs, even though it means more things for us to do! It means there is something we didn't think of or test in the particular module and we won't know about this unless you tell us. The Bugzilla system requires you register to avoid spam and to allow us to contact you again when the bug is fixed or to clarify the problem and solutions.
It is important that you record the version of BioPerl you are running (if you don't know, see the FAQ the question is addressed there). You can also include the version of Perl you are using and the Operating System you are running.
Simon Tatham has a great resource on how to effectively report bugs.
Submitting Bugs
When submitting new bugs on Bugzilla, enter a brief description and other general information. Do not paste data or scripts into the description field!
After the report is generated, you can create attachments for any relevant data, code, or patches for the bug using the 'Create a New Attachment' link on the bug report page.
Submitting Patches
We gladly welcome patches. Try to ensure the patch is derived against the latest code checked out from Subversion, particularly if the patch is large.
Submitting New Modules and Code Snippets
We also accept new code, either as full-fledged modules or as snippets of code (snippets work better as a patch). It helps to include a test case (using Test::More following our testing standards in our Writing_BioPerl_Tests HOWTO).
Etiquette
Good bug reports are ones which provide a small amount of code and the necessary test files to reproduce your bug. By doing this work up front you insure the developer spends most of his or her time actually working on the problem. Pasting your entire 600 line program into the comment buffer is probably not going to get an enthusiastic response. In addition, isolating the problem down to a small amount of your code will help ensure that the bug is not on your end before we dive in and start working on it.
Open Bugs
This list details the open Bugs on Bugzilla for BioPerl.
Bugzilla Bugs
- [Bug 2537] num_conserved reports incorrect value during FASTA34 parsing
- [Bug 2069] Bio::Tools:pSW stop codon bug
- [Bug 2213] crashes on downloading NCBI records
- [Bug 2513] creating a Bio::SeqFeature::Annotation object downloads the entire so.obo
- [Bug 2545] bioperl nightly build script svn failure on lock
- [Bug 2142] conservative/radical nonsynonymous distances method in Bio::Align::DNAStatistics
- [Bug 2156] Bio::DB::REBASE module and t/DBREBASE.t test script
- [Bug 2247] Have Bio::SearchIO::blast methods available for other BLAST parsers
- [Bug 2262] Bio::Seq object loses sequence data when blessed as Bio::Seq::Meta::Array
- [Bug 2275] GO Upload with bp_load_ontology.pl throws errors
- [Bug 2280] crash on the attempt to store same sequence in a diff. namespace
- [Bug 2281] unable to copy a sequence from one namespace to another one
- [Bug 2326] bp_fast_load_gff creates mostly empty tables.
- [Bug 2346] exonerate parser in bioperl-live fails when protein2dna comparison is performed
- [Bug 2350] Make ID system consistent between Bio::Align::AlignI and Bio::SeqI
- [Bug 2370] Bio::Assembly::Scaffold Source
- [Bug 2373] Handling of multiple species or hybrid species in EMBL records
- [Bug 2376] ID of match features in bp_search2gff.pl
- [Bug 2377] Target tag format in bp_search2gff.pl
- [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score
- [Bug 2429] Bio::FeatureIO gff3 fails to parse canonical GFF3 file from GFF3 spec
- [Bug 2439] multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO
- [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values
- [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface
- [Bug 2472] postgreSQL v8.3 automatic casts limited may necessitate explicit cast
- [Bug 2474] postgres 8.3 - load_seqdatabase.pl / swissprot
- [Bug 2476] "Undefined sub-sequence" when processing tblastx output
- [Bug 2482] paml4 mlc file fails to parse
- [Bug 2483] request for implementation of write_assembly
- [Bug 2498] Add HSP sorting to Bio::Search::Hit
- [Bug 2505] Add in a sort feature for SeqFeatureI get_all_tags()
- [Bug 2514] Run tests with binaries installed
- [Bug 2515] GenBank XML parser
- [Bug 2575] Easy request - a frac_identical_total column in HSPTableWriter.pm?
- [Bug 2594] Bio::Species memory leak
- [Bug 2599] DBLINK to replace PROJECT for GenBank format annotation
- [Bug 2615] Argument inconsistency in Bio::SearchIO
- [Bug 2620] Bio::Assembly::IO::phrap is incomplete
- [Bug 2636] New version of PAML changes output
- [Bug 2641] hook stomp in bioperl.lisp
- [Bug 2642] bioperl.lisp, 2 empty lines before '=cut' in templates
- [Bug 2648] The results of "Bio::Assembly::Scaffold->get_all_seq_ids" does NOT behave as documented
- [Bug 2668] bioperl-ext fails to compile on x86_64
- [Bug 1857] Bio::SearchDist (Bio::Ext::Align) reports incorrect E-values
- [Bug 2322] bp_genbank2gff3.pl doesn't calculate CDS phases
- [Bug 2567] AlignIO::stockholm concatenates sequences
- [Bug 1572] no docs and possible typo in Bio::Location::Simple/Atomic::trunc
- [Bug 1877] Bio::PopGen::IO::hapmap.pm write_population method
- [Bug 2092] Can't store proteins with species using bioperl-db
- [Bug 2127] Add Amap, Kalign and Probcon Quiet option
- [Bug 2278] FASTA m10 output support
- [Bug 2345] Get mappable sequence coords after removing alignment columns
- [Bug 2347] Bio::Tools::Run::Phylo::PAML::Baseml needs polishing and completion
- [Bug 1508] SeqIO allows fasta to masquerade as genbank or gcg or ace
- [Bug 843] _readline() in SeqIO.pm
- [Bug 1514] TCoffee parse score_ascii
- [Bug 1528] Removing sequences from mysql using bioentry-id
- [Bug 1874] fixedtopo random tree Bio::Tree::RandomFactory
- [Bug 1881] implement Bio::PopGen::IO::haploview.pm
- [Bug 1891] Implement a seqgen wrapper in bioperl-run
- [Bug 2070] mumsa wrapper
- [Bug 2078] informative codons method for kaks -- Bio/Align/DNAStatistics.pm
- [Bug 2126] t/Pise.t warning
- [Bug 2663] seq_inds overhaul
- [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2
- [Bug 2336] bp_bioflat_index.pl and Bio::DB::Flat::BDB::fasta creates incorrect index
- [Bug 2337] BDB flatfile index should store global configuration data in BDB
- [Bug 2338] The first 4 bytes of flatfile index is wrong (--indextype flat)
- [Bug 2339] In a flat file index, the size of the final entry of a fasta file is wrong
- [Bug 2573] Ontology tests failing
- [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates
- [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta
- [Bug 2637] new modules for HIV sequence queries
- [Bug 2673] original fields not inherited by seq objects in alignment slices
- [Bug 2450] Clean up AlignIO::stockholm output, complete annotation parsing
- [Bug 2343] Support for floating point positions in Bio::Graphic::*
- [Bug 2365] Add support for making the image background transparent
- [Bug 2018] Bio::ClusterIO::dbsnp breaks with new XML output
- [Bug 2021] Unimplemented methods in Bio::Assembly classes
- [Bug 2329] Enhancement to Bio::SeqIO::abi - abi_with_trace
- [Bug 2492] Method "pi" in package Bio::PopGen::Statistics
- [Bug 2577] Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit
- [Bug 2074] bioperl-ext: make test fails using io_lib v. 1.9 or higher
