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Branch: master

Merge pull request #101 from christiam/master

Expand RemoteBlast synopsis sample code.  Merge seems like it should be fine (travis fails may be unrelated)
latest commit db8b57dcd6
@cjfields cjfields authored
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Align
AlignIO all "nexml.pm": Fixed subroutines calling "Bio::Phylo::IO->parse".
Annotation changes all issue tracking in preparation for switch to github issues
Assembly Only return true values and undef from READLINE in scalar context
Cluster changes all issue tracking in preparation for switch to github issues
ClusterIO changes all issue tracking in preparation for switch to github issues
CodonUsage changes all issue tracking in preparation for switch to github issues
DB
Das changes all issue tracking in preparation for switch to github issues
Draw changes all issue tracking in preparation for switch to github issues
Event changes all issue tracking in preparation for switch to github issues
Factory FTLocationFactory.pm: Fixed a long-standing issue at "from_string()"
Index
LiveSeq changes all issue tracking in preparation for switch to github issues
Location Bio/Location/Split.pm: Final fix for issue #76. From now on,
Map changes all issue tracking in preparation for switch to github issues
MapIO changes all issue tracking in preparation for switch to github issues
Matrix
MolEvol
Nexml changes all issue tracking in preparation for switch to github issues
Ontology Minor edits
OntologyIO
Phenotype
PhyloNetwork
PopGen Only return true values and undef from READLINE in scalar context
Restriction changes all issue tracking in preparation for switch to github issues
Root changes all issue tracking in preparation for switch to github issues
Search
SearchIO hmmmer2 & hmmer3: Complete elimination of the use of '$_'
Seq changes all issue tracking in preparation for switch to github issues
SeqEvolution
SeqFeature Bio/SeqFeature/Generic.pm: Fix for issue #76, adjusted "seq"
SeqIO Accept space after equal sign in qualifiers when reading EMBL.
Structure Only return true values and undef from READLINE in scalar context
Symbol changes all issue tracking in preparation for switch to github issues
Taxonomy changes all issue tracking in preparation for switch to github issues
Tools
Tree changes all issue tracking in preparation for switch to github issues
TreeIO all "nexml.pm": Fixed subroutines calling "Bio::Phylo::IO->parse".
Variation changes all issue tracking in preparation for switch to github issues
AlignIO.pm Only return true values and undef from READLINE in scalar context
AnalysisI.pm changes all issue tracking in preparation for switch to github issues
AnalysisParserI.pm changes all issue tracking in preparation for switch to github issues
AnalysisResultI.pm changes all issue tracking in preparation for switch to github issues
AnnotatableI.pm changes all issue tracking in preparation for switch to github issues
AnnotationCollectionI.pm
AnnotationI.pm changes all issue tracking in preparation for switch to github issues
ClusterI.pm
ClusterIO.pm
DBLinkContainerI.pm changes all issue tracking in preparation for switch to github issues
DasI.pm
DescribableI.pm changes all issue tracking in preparation for switch to github issues
FeatureHolderI.pm changes all issue tracking in preparation for switch to github issues
HandlerBaseI.pm changes all issue tracking in preparation for switch to github issues
IdCollectionI.pm changes all issue tracking in preparation for switch to github issues
IdentifiableI.pm changes all issue tracking in preparation for switch to github issues
LocatableSeq.pm changes all issue tracking in preparation for switch to github issues
LocationI.pm changes all issue tracking in preparation for switch to github issues
MapIO.pm changes all issue tracking in preparation for switch to github issues
NexmlIO.pm all "nexml.pm": Fixed subroutines calling "Bio::Phylo::IO->parse".
OntologyIO.pm changes all issue tracking in preparation for switch to github issues
ParameterBaseI.pm changes all issue tracking in preparation for switch to github issues
Perl.pm changes all issue tracking in preparation for switch to github issues
PhyloNetwork.pm some ambiguity issues with this method call for some reason (namespac…
PrimarySeq.pm
PrimarySeqI.pm Darn you, emacs, putting tab characters in. Sorry, didn't realize I h…
PullParserI.pm
Range.pm
RangeI.pm changes all issue tracking in preparation for switch to github issues
SearchDist.pm changes all issue tracking in preparation for switch to github issues
SearchIO.pm Only return true values and undef from READLINE in scalar context
Seq.pm Minor doc fixes
SeqAnalysisParserI.pm changes all issue tracking in preparation for switch to github issues
SeqFeatureI.pm
SeqI.pm changes all issue tracking in preparation for switch to github issues
SeqIO.pm Only return true values and undef from READLINE in scalar context
SeqUtils.pm
SimpleAlign.pm
SimpleAnalysisI.pm
Species.pm
Taxon.pm all key tests pass (only a few haven't been checked), but likely need…
Taxonomy.pm changes all issue tracking in preparation for switch to github issues
TreeIO.pm Only return true values and undef from READLINE in scalar context
UpdateableSeqI.pm changes all issue tracking in preparation for switch to github issues
WebAgent.pm
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