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Changes file update

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commit 40cdfdc5e78dc72c9e74b1fdf567b3cf4754163c 1 parent 739a653
@fangly fangly authored
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@@ -19,6 +19,33 @@ CPAN releases are branched from 'master'.
1.?.?
+ [New features]
+
+ * Bio::Seq::SimulatedRead
+ - New module to represent reads taken from other sequences [fangly]
+ * Bio::Root::IO
+ - Moved the format() and variant() methods from Bio::*IO modules to
+ Bio::Root::IO [fangly]
+ - Can now use format() to get the type of IO format in use [fangly]
+ * Bio::Tools::IUPAC
+ - New regexp() method to create regular expressions from IUPAC sequences
+ [fangly]
+ * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
+ - Code refresh [fangly]
+ * Bio::DB::Taxonomy
+ - Added support for the Greengenes and Silva taxonomies [fangly]
+ * Bio::Tree::TreeFunctionsI
+ - get_lineage_string() represents a lineage as a string [fangly]
+ - add_trait() returns instead of reporting an error when the column
+ number is exceeded in add_trait() [fangly]
+ - Option to support tree leaves without trait [fangly]
+ - Allow ID of 0 in trait files [fangly]
+ * Bio::DB::Taxonomy::list
+ - Misc optimizations [fangly]
+ - Option -names of get_taxon() to help with ambiguous taxa [fangly]
+ * Bio::DB::Taxonomy::*
+ - get_num_taxa() returns the number of taxa in the database [fangly]
+
[Bug fixes]
* [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
@@ -30,6 +57,29 @@ CPAN releases are branched from 'master'.
* Various fixes for Stockholm file indexing and processing [bosborne]
* Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
breaks parsing [cjfields]
+ * Fix case where Bio::Seq::Meta* objects with no meta information could not
+ be reverse-complemented [fangly]
+ * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
+ * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
+ when unsure that values will be numerical [fangly]
+ * Fix undef warnings in Bio::SeqIO::embl [fangly]
+ * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
+ * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
+ Sallou]
+ * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
+ source_tag and display_name must return a string, not undef [fangly]
+ * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
+ add_SeqFeature takes a single argument [fangly]
+ * Use cross-platform filenames and temporary directory in
+ Bio::DB::Taxonomy::flatfile [fangly]
+ * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
+ properly identified as existing taxa in the database [fangly]
+ * Fix issue where a Bio::DB::Taxonomy::list object could not be created
+ without also passing a lineage to store [fangly]
+ * Prevent passing a directory to the gi2taxid option (-g) of
+ bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
+ [fangly]
+
1.6.901 May 18, 2011
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