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Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
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bp_load_gff.pl will not shut up
#53
cjfields
opened
8 years ago
3
bp_load_ontology ISBN title parsing error in OBO format
#52
cjfields
opened
8 years ago
1
[TODO] LocatableSeq symbols are globally set (should be localized)
#51
cjfields
opened
8 years ago
2
Bio::Tools::Run::StandAloneBlast does not quote shell metacharacters in filenames, but Bio::SearchIO::blast does
#50
cjfields
opened
8 years ago
3
New MUMmer AlignIO support
#49
cjfields
opened
8 years ago
18
global verbosity does not propagate to new objects post-set
#48
cjfields
opened
8 years ago
5
LocatableSeq::subseq with mapping and frameshift functionality
#47
cjfields
opened
8 years ago
5
LocatableSeq::subseq with mapping and frameshift functionality
#46
cjfields
closed
8 years ago
3
WU-BLAST XML support
#45
cjfields
opened
8 years ago
7
bioperl-ext fails to compile on x86_64
#44
cjfields
opened
8 years ago
3
Bio::Assembly::IO::phrap is incomplete
#43
cjfields
opened
8 years ago
1
Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit
#42
cjfields
opened
8 years ago
5
creating a Bio::SeqFeature::Annotation object downloads the entire so.obo
#41
cjfields
opened
8 years ago
4
Add in a sort feature for SeqFeatureI get_all_tags()
#40
cjfields
opened
8 years ago
1
Add HSP sorting to Bio::Search::Hit
#39
cjfields
opened
8 years ago
5
"Undefined sub-sequence" when processing tblastx output
#38
cjfields
opened
8 years ago
36
postgres 8.3 - load_seqdatabase.pl / swissprot
#37
cjfields
opened
8 years ago
4
postgreSQL v8.3 automatic casts limited may necessitate explicit cast
#36
cjfields
opened
8 years ago
1
multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO
#35
cjfields
opened
8 years ago
7
Bio::FeatureIO gff3 fails to parse canonical GFF3 file from GFF3 spec
#34
cjfields
opened
8 years ago
3
Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score
#33
cjfields
opened
8 years ago
17
Target tag format in bp_search2gff.pl
#32
cjfields
opened
8 years ago
2
ID of match features in bp_search2gff.pl
#31
cjfields
opened
8 years ago
2
Handling of multiple species or hybrid species in EMBL records
#30
cjfields
opened
8 years ago
5
Bio::Assembly::Scaffold Source
#29
cjfields
opened
8 years ago
6
Add support for making the image background transparent
#28
cjfields
opened
8 years ago
6
Get mappable sequence coords after removing alignment columns
#27
cjfields
opened
8 years ago
1
Support for floating point positions in Bio::Graphic::*
#26
cjfields
opened
8 years ago
7
Enhancement to Bio::SeqIO::abi - abi_with_trace
#25
cjfields
opened
8 years ago
14
bp_fast_load_gff creates mostly empty tables.
#24
cjfields
opened
8 years ago
1
bp_genbank2gff3.pl doesn't calculate CDS phases
#23
cjfields
opened
8 years ago
2
crash on the attempt to store same sequence in a diff. namespace
#22
cjfields
opened
8 years ago
4
FASTA m10 output support
#21
cjfields
opened
8 years ago
7
GO Upload with bp_load_ontology.pl throws errors
#20
cjfields
opened
8 years ago
3
Bio::Seq object loses sequence data when blessed as Bio::Seq::Meta::Array
#19
cjfields
opened
8 years ago
4
Have Bio::SearchIO::blast methods available for other BLAST parsers
#18
cjfields
opened
8 years ago
3
crashes on downloading NCBI records
#17
cjfields
opened
8 years ago
15
conservative/radical nonsynonymous distances method in Bio::Align::DNAStatistics
#16
cjfields
opened
8 years ago
1
Add Amap, Kalign and Probcon Quiet option
#15
cjfields
opened
8 years ago
2
informative codons method for kaks -- Bio/Align/DNAStatistics.pm
#14
cjfields
opened
8 years ago
3
bioperl-ext: make test fails using io_lib v. 1.9 or higher
#13
cjfields
opened
8 years ago
20
mumsa wrapper
#12
cjfields
opened
8 years ago
2
Bio::Tools:pSW stop codon bug
#11
cjfields
opened
8 years ago
5
Unimplemented methods in Bio::Assembly classes
#10
cjfields
opened
8 years ago
8
Bio::ClusterIO::dbsnp breaks with new XML output
#9
cjfields
opened
8 years ago
17
Implement a seqgen wrapper in bioperl-run
#8
cjfields
opened
8 years ago
2
implement Bio::PopGen::IO::haploview.pm
#7
cjfields
opened
8 years ago
2
Bio::PopGen::IO::hapmap.pm write_population method
#6
cjfields
opened
8 years ago
3
fixedtopo random tree Bio::Tree::RandomFactory
#5
cjfields
opened
8 years ago
1
Bio::SearchDist (Bio::Ext::Align) reports incorrect E-values
#4
cjfields
opened
8 years ago
6
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