bioperl bioperl-live-redmine issues - Githubissues

bioperl / bioperl-live-redmine

Legacy tickets migrated from the OBF Redmine issue tracker: http://redmine.open-bio.org

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Bio::DB::Taxonomy::flatfile.pm - temporary files at /var/tmp/DBD*

#153 cjfields opened 9 years ago
3
Bio::Tools::Primer3 - Exception raised with Primer3 2.3.X

#152 cjfields closed 8 years ago
3
Bio::SeqIO Interproscan XML parsing issue

#151 cjfields opened 9 years ago
3
Bio::DB::EntrezGene no longer returning gene names via get_Stream_by_id

#150 cjfields opened 9 years ago
2
Bio::Biblio example doesn't work

#149 cjfields opened 9 years ago
0
Reducing the time complexity of Bio/TreeIO/NewickParser.pm

#148 cjfields opened 9 years ago
3
Documentation auto-generated from github repository is out-of-date

#147 cjfields opened 9 years ago
2
Bio::Assembly::IO can not correctly parse all ace contig ids

#146 cjfields opened 9 years ago
0
Bio::DB::Taxonomy look under a root node for get_taxon

#145 cjfields opened 9 years ago
0
Bio::SeqIO unable to parse "PIR" format sequence with no description line

#144 cjfields opened 9 years ago
2
get_lca() test mixing local and remote databases not working

#143 cjfields opened 9 years ago
0
Bio::DB::GenBank/GenPept get_Seq/Stream_by_id no longer retrieves LOCUS IDs

#142 cjfields opened 9 years ago
2
Failed to add annotation in Bio::TreeIO for the phyloXML format

#141 cjfields opened 9 years ago
0
incorrect documentation of bioperl-run TCoffee module

#140 cjfields opened 9 years ago
0
Making Bio::DB::Fasta Storable and thread safe

#139 cjfields opened 9 years ago
4
processed_transcript glyph no longer handles Bio::SeqFeature::Gene::Exon features

#138 cjfields opened 9 years ago
1
Bio::Tools::Phylo::PAML::yn00 adds a sequence in the output file of PAML 4.5

#137 cjfields opened 9 years ago
1
PAML parse_PairwiseCodon doesn't parse the ML results correctly

#136 cjfields opened 9 years ago
3
PAML parse_seqs misses the first sequence in the mlc file

#135 cjfields opened 9 years ago
2
codeml sometimes fails to parse if sequence name is too long

#134 cjfields opened 9 years ago
1
Codeml (v 4v4d) using fixed kappa value, reports wrong kappa

#133 cjfields opened 9 years ago
2
segregating sites calculation fails on gapped sequences

#132 cjfields opened 9 years ago
0
Bio::SeqIO GenBank files not entirely up to spec.

#131 cjfields opened 9 years ago
4
blast2sam

#130 cjfields opened 9 years ago
3
Bio::Tools::Run::StandAloneBlastPlus --remote database with '/' separator

#129 cjfields opened 9 years ago
1
Bio::SearchIO : bug when parsing TBlastX and method matches of Bio::SearchIO::Hit

#128 cjfields opened 9 years ago
0
Bio::FeatureIO::gff::_handle_feature bug in method

#127 cjfields opened 9 years ago
3
Fu and Li's D crashes when $n <=3

#126 cjfields opened 9 years ago
1
Installation problem with ppm

#125 cjfields opened 9 years ago
1
AlignIO MSF writing

#124 cjfields opened 9 years ago
0
Bio::CodonUsage::Table from Bio::DB::CUTG lack relative frequencies

#123 cjfields opened 9 years ago
3
Meta.{json,yml} bug in BioPerl-1.6.901.tar.gz on cpan

#122 cjfields opened 9 years ago
0
fasta35 and fasta36 parsing support in BioPerl

#121 cjfields opened 9 years ago
1
Bio::DB::WebDBSeqI::get_Stream_by_id

#120 cjfields opened 9 years ago
0
SearchIO::infernal.pm: parser->next_result deliveres only one result from mulit-CM infernal report

#119 cjfields opened 9 years ago
1
FASTQ indexing borked with qual strings starting with '@'

#118 cjfields opened 9 years ago
1
genbank2gff3.pl error when running on multiple input files

#117 cjfields opened 9 years ago
1
Bio::Tools::Run::Phylo::Phyml, tree_string

#116 cjfields opened 9 years ago
0
BioPerl(Bio::SearchIO) has different behaviours in parsing blast and blast+ result

#115 cjfields opened 9 years ago
3
Test bug

#114 cjfields opened 9 years ago
1
incomplete parse of entrezgene file

#113 cjfields opened 9 years ago
2
Undocumented need for Array::Compare.

#112 cjfields opened 9 years ago
2
Error in FASTA sequence retrival using Bio::DB::FASTA->subseq()

#111 cjfields opened 9 years ago
6
Author tracking across repository migrations

#110 cjfields opened 9 years ago
0
Bio::Tools::Run::Phylo::Phyml Lacks LG model of AA sequence evolution

#109 cjfields opened 9 years ago
0
version() not implemented for Bio::Tools::Run::StandAloneBlastPlus

#108 cjfields opened 9 years ago
0
Bio::Tools::Run::StandAloneBlastPlus tests failing with latest BLAST+

#107 cjfields opened 9 years ago
3
Bio::Tools::Run::BWA failing tests

#106 cjfields opened 9 years ago
0
Bio::AlignIO::nexml doesn't work with NeXML 0.9 and Bio::Phylo

#105 cjfields opened 9 years ago
0
Bio::SeqIO::nexml doesn't work with NeXML 0.9 and Bio::Phylo

#104 cjfields opened 9 years ago
1