issues
search
bioperl
/
bioperl-live-redmine
Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org
0
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Bio::SeqIO::nexml doesn't work with NeXML 0.9 and Bio::Phylo
#103
cjfields
closed
8 years ago
1
NeXML tests need updating to v 0.9 for Bio::Phylo compat
#102
cjfields
opened
8 years ago
0
Use of uninitialized value in length at Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1064.
#101
cjfields
opened
8 years ago
3
file/fh checking should be in Bio::Root::IO, not in subclasses
#100
cjfields
opened
8 years ago
1
Bio::Tools::Run::Phylo::Phyml -- documented values for -f parameter
#99
cjfields
opened
8 years ago
0
Bio::Tools::Run::Phylo::Phyml -- Bootstrap and other confidence measures
#98
cjfields
opened
8 years ago
0
Bio::DB::GenBank keeping child process ID's
#97
cjfields
opened
8 years ago
1
calculate CDS phase when converting GenBank to GFF
#96
cjfields
opened
8 years ago
0
Need to change Bugzilla macro in Wiki
#95
cjfields
opened
8 years ago
1
Consider interfacing with TABIX for feature file indexing and lookup for bed, gff, vcf format files.
#94
cjfields
opened
8 years ago
1
Bio::Index::Fastq indexing not in sync with FASTQ spec
#93
cjfields
opened
8 years ago
1
SearchIO:blastxml does not return correct query name for blastp (2.2.24)
#92
cjfields
opened
8 years ago
5
Order of elements in phyloXML
#91
cjfields
opened
8 years ago
2
Bio::Tools::Run::StandAloneBlastPlus "entrez_query" option
#90
cjfields
opened
8 years ago
3
Error with TreeIO for NHX format
#89
cjfields
opened
8 years ago
6
bp_genbank2gff3.pl, inconsistent strands for Trans-spliced gene.
#88
cjfields
opened
8 years ago
1
Problems with Bio::LocatableSeq::length() and strand()
#87
cjfields
opened
8 years ago
1
bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3
#86
cjfields
opened
8 years ago
2
-task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus
#85
cjfields
opened
8 years ago
0
seq_version() in Bio::PrimarySeq not found
#84
cjfields
opened
8 years ago
4
bam assys: no sequence in opposite oriented reads
#83
cjfields
opened
8 years ago
8
Bio::Tools::GFF: empty group tag hash
#82
cjfields
opened
8 years ago
1
Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters
#81
cjfields
opened
8 years ago
1
Bio::Tools::Run::Genewise doesn't accept parameters as described in its documentation
#80
cjfields
opened
8 years ago
0
get_tiled_alns() skips first HSP
#79
cjfields
opened
8 years ago
4
AlignIO hash sequence storage
#78
cjfields
opened
8 years ago
3
Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above
#77
cjfields
opened
8 years ago
3
GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column
#76
cjfields
opened
8 years ago
3
BioPerl breaks listing of updateable modules in a CPAN shell
#75
cjfields
opened
8 years ago
3
AlignIO::fasta should not flush sequences to alignment
#74
cjfields
opened
8 years ago
4
Bio::TreeIO::nhx cannot parse empty [&&NHX] + round-trip failure
#73
cjfields
opened
8 years ago
1
[TODO] Add tests for Mitch's patch to Bio::DB::SeqFeature::Store
#72
cjfields
opened
8 years ago
0
Reconciling RangeI methods for split and fuzzy locations
#71
cjfields
opened
8 years ago
0
SeqFeature with different sequence IDs but same range return true with overlaps()
#70
cjfields
opened
8 years ago
1
New package Phylip/Pars.pm
#69
cjfields
opened
8 years ago
4
ProtPars.t passing but with lots of warnings
#68
cjfields
opened
8 years ago
2
Parsing multiple contig EMBL records (CO lines instead of SQ lines)
#67
cjfields
opened
8 years ago
15
hss memory allocation 1-off error in HMM.xs::HMM_viterbi
#66
cjfields
opened
8 years ago
1
Bio::Tools::GFF, Target Tag disappears when editing a gff3 file
#65
cjfields
opened
8 years ago
3
NodeMod issue
#64
cjfields
opened
8 years ago
3
PPM issues on Windows (assuming Activeperl)
#63
cjfields
opened
8 years ago
0
Bio::Search::HSP::FastaHSP -> get_aln -> Bio::Locatable end is float
#62
cjfields
opened
8 years ago
7
Some of the scripts linked here are not found
#61
cjfields
opened
8 years ago
8
it is better to update the Bio::Tools::RepeatMasker module
#60
cjfields
opened
8 years ago
3
ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail
#59
cjfields
opened
8 years ago
1
bp_search2gff.pl's --component option is a fail
#58
cjfields
opened
8 years ago
2
support for HPRD PSI-MI 2.5 XML, was: Bioperl-network parsing error
#57
cjfields
opened
8 years ago
2
Trace data in Bio::SeqIO::scf appears scrambled
#56
cjfields
opened
8 years ago
1
Bio::SeqIO::embl->next_seq corrupted with "Segmentation fault" when parsing million-line entries
#55
cjfields
opened
8 years ago
7
[TODO] Refactor Bio::FeatureIO
#54
cjfields
opened
8 years ago
1
Previous
Next