[med-svn] [bioperl] 03/06: Update upstream source from tag 'upstream/1.7.2'
Andreas Tille
tille at debian.org
Sun Dec 3 18:00:41 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository bioperl.
commit a33ec2f4463f54956ecdaef28445249b384aee35
Merge: 51c2815 469af47
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 18:53:23 2017 +0100
Update upstream source from tag 'upstream/1.7.2'
Update to upstream version '1.7.2'
with Debian dir 5fdd6584523db8939f892f296b7b70ebd3512ab0
.travis.yml | 81 +-
Bio/AlignIO/phylip.pm | 529 +++---
Bio/AlignIO/xmfa.pm | 30 +-
Bio/AnalysisI.pm | 2 +-
Bio/Annotation/OntologyTerm.pm | 2 +-
Bio/AnnotationCollectionI.pm | 2 +-
Bio/Assembly/Contig.pm | 40 +-
Bio/Assembly/ScaffoldI.pm | 2 +-
Bio/Assembly/Singlet.pm | 2 +-
Bio/Assembly/Tools/ContigSpectrum.pm | 2 +-
Bio/Cluster/UniGene.pm | 4 +-
Bio/DB/EMBL.pm | 2 +-
Bio/DB/Fasta.pm | 2 +-
Bio/DB/Flat/BinarySearch.pm | 2 +-
Bio/DB/GFF.pm | 6 +-
Bio/DB/GFF/Adaptor/dbi.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysql.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/mysqlcmap.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/oracle.pm | 2 +-
Bio/DB/GFF/Adaptor/dbi/pg.pm | 2 +-
Bio/DB/GFF/Segment.pm | 6 +-
Bio/DB/GenBank.pm | 2 +-
Bio/DB/GenPept.pm | 2 +-
Bio/DB/GenericWebAgent.pm | 24 +-
Bio/DB/HIV/HIVQueryHelper.pm | 2 +-
Bio/DB/IndexedBase.pm | 78 +-
Bio/DB/LocationI.pm | 20 +-
Bio/DB/MeSH.pm | 4 +-
Bio/DB/Qual.pm | 2 +-
Bio/DB/Query/HIVQuery.pm | 2 +-
Bio/DB/RefSeq.pm | 4 +-
Bio/DB/ReferenceI.pm | 20 +-
Bio/DB/Registry.pm | 38 +-
Bio/DB/SeqFeature/Store.pm | 2 +-
Bio/DB/SeqFeature/Store/DBI/SQLite.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF2Loader.pm | 2 +-
Bio/DB/SeqFeature/Store/GFF3Loader.pm | 6 +-
Bio/DB/SeqFeature/Store/Loader.pm | 2 +-
Bio/DB/TFBS/transfac_pro.pm | 8 +-
Bio/DB/Taxonomy/entrez.pm | 122 +-
Bio/DB/Taxonomy/flatfile.pm | 2 +-
Bio/DB/Taxonomy/sqlite.pm | 6 +-
Bio/DB/WebDBSeqI.pm | 4 +-
Bio/DescribableI.pm | 2 +-
Bio/Factory/ApplicationFactoryI.pm | 12 +-
Bio/Factory/ObjectFactoryI.pm | 2 +-
Bio/Index/Abstract.pm | 68 +-
Bio/Index/AbstractSeq.pm | 2 +-
Bio/Index/Blast.pm | 60 +-
Bio/Index/BlastTable.pm | 52 +-
Bio/Index/Hmmer.pm | 54 +-
Bio/Index/Stockholm.pm | 6 +-
Bio/LiveSeq/IO/Loader.pm | 2 +-
Bio/LiveSeq/IO/README | 2 +-
Bio/LiveSeq/Mutation.pm | 2 +-
Bio/LiveSeq/SeqI.pm | 4 +-
Bio/LocatableSeq.pm | 2 +-
Bio/Location/Atomic.pm | 10 +-
Bio/Location/Fuzzy.pm | 2 +-
Bio/Location/FuzzyLocationI.pm | 2 +-
Bio/Location/Simple.pm | 6 +-
Bio/Location/Split.pm | 2 +-
Bio/Location/SplitLocationI.pm | 2 +-
Bio/LocationI.pm | 2 +-
Bio/Map/CytoMarker.pm | 2 +-
Bio/Map/CytoPosition.pm | 6 +-
Bio/Map/GeneRelative.pm | 4 +-
Bio/Map/Microsatellite.pm | 2 +-
Bio/Map/OrderedPosition.pm | 2 +-
Bio/Map/Physical.pm | 2 +-
Bio/Map/Position.pm | 2 +-
Bio/Map/PositionI.pm | 2 +-
Bio/Map/Relative.pm | 2 +-
Bio/Map/TranscriptionFactor.pm | 2 +-
Bio/Matrix/Generic.pm | 6 +-
Bio/Matrix/PSM/IO.pm | 2 +-
Bio/Matrix/PSM/IO/masta.pm | 6 +-
Bio/Matrix/PSM/InstanceSite.pm | 2 +-
Bio/Matrix/PSM/ProtMatrix.pm | 6 +-
Bio/Matrix/PSM/ProtPsm.pm | 2 +-
Bio/Matrix/PSM/Psm.pm | 4 +-
Bio/Matrix/PSM/PsmI.pm | 4 +-
Bio/Matrix/PSM/SiteMatrix.pm | 12 +-
Bio/Matrix/PSM/SiteMatrixI.pm | 4 +-
Bio/Ontology/OntologyStore.pm | 2 +-
Bio/Ontology/SimpleOntologyEngine.pm | 2 +-
Bio/Ontology/Term.pm | 4 +-
Bio/Ontology/TermI.pm | 2 +-
Bio/OntologyIO/Handlers/BaseSAXHandler.pm | 26 +-
Bio/OntologyIO/Handlers/InterPro_BioSQL_Handler.pm | 4 +-
Bio/OntologyIO/obo.pm | 22 +-
Bio/ParameterBaseI.pm | 22 +-
Bio/Perl.pm | 2 +-
Bio/PopGen/HtSNP.pm | 6 +-
Bio/PopGen/Individual.pm | 2 +-
Bio/PopGen/Population.pm | 4 +-
Bio/PopGen/TagHaplotype.pm | 4 +-
Bio/PrimarySeq.pm | 10 +-
Bio/PrimarySeqI.pm | 8 +-
Bio/PullParserI.pm | 2 +-
Bio/Restriction/Analysis.pm | 2 +-
Bio/Restriction/Enzyme.pm | 2 +-
Bio/Restriction/EnzymeI.pm | 2 +-
Bio/Restriction/IO/base.pm | 6 +-
Bio/Restriction/IO/itype2.pm | 2 +-
Bio/Root/Exception.pm | 2 +-
Bio/Root/Root.pm | 2 +-
Bio/Root/Storable.pm | 4 +-
Bio/Root/Test.pm | 6 +-
Bio/Root/Utilities.pm | 10 +-
Bio/Root/Version.pm | 2 +-
Bio/Search/BlastUtils.pm | 2 +-
Bio/Search/HSP/BlastPullHSP.pm | 2 +-
Bio/Search/HSP/GenericHSP.pm | 2 +-
Bio/Search/HSP/HMMERHSP.pm | 2 +-
Bio/Search/HSP/HSPI.pm | 2 +-
Bio/Search/HSP/ModelHSP.pm | 2 +-
Bio/Search/HSP/PullHSPI.pm | 2 +-
Bio/Search/Hit/GenericHit.pm | 2 +-
Bio/Search/Hit/HMMERHit.pm | 2 +-
Bio/Search/Hit/ModelHit.pm | 2 +-
Bio/Search/Iteration/IterationI.pm | 2 +-
Bio/Search/SearchUtils.pm | 2 +-
Bio/Search/Tiling/TilingI.pm | 2 +-
Bio/SearchDist.pm | 2 +-
Bio/SearchIO.pm | 58 +-
Bio/SearchIO/Writer/HTMLResultWriter.pm | 2 +-
Bio/SearchIO/Writer/TextResultWriter.pm | 2 +-
Bio/SearchIO/exonerate.pm | 2 +-
Bio/SearchIO/fasta.pm | 48 +-
Bio/SearchIO/hmmer3.pm | 2 +-
Bio/Seq.pm | 6 +-
Bio/Seq/EncodedSeq.pm | 2 +-
Bio/Seq/Meta/Array.pm | 4 +-
Bio/Seq/MetaI.pm | 8 +-
Bio/Seq/PrimaryQual.pm | 4 +-
Bio/Seq/PrimedSeq.pm | 2 +-
Bio/Seq/QualI.pm | 8 +-
Bio/Seq/RichSeqI.pm | 2 +-
Bio/Seq/SeqBuilder.pm | 4 +-
Bio/Seq/SeqWithQuality.pm | 14 +-
Bio/Seq/SequenceTrace.pm | 6 +-
Bio/Seq/SimulatedRead.pm | 2 +-
Bio/SeqFeature/AnnotationAdaptor.pm | 46 +-
Bio/SeqFeature/Computation.pm | 6 +-
Bio/SeqFeature/Generic.pm | 4 +-
Bio/SeqFeature/Lite.pm | 2 +-
Bio/SeqFeature/PositionProxy.pm | 2 +-
Bio/SeqFeature/SubSeq.pm | 2 +-
Bio/SeqFeature/Tools/Unflattener.pm | 2 +-
Bio/SeqFeature/TypedSeqFeatureI.pm | 2 +-
Bio/SeqIO.pm | 24 +-
Bio/SeqIO/ace.pm | 2 +-
Bio/SeqIO/bsml.pm | 20 +-
Bio/SeqIO/chadoxml.pm | 4 +-
Bio/SeqIO/chaos.pm | 2 +-
Bio/SeqIO/embl.pm | 6 +-
Bio/SeqIO/fasta.pm | 2 +-
Bio/SeqIO/fastq.pm | 2 +-
Bio/SeqIO/game/gameHandler.pm | 2 +-
Bio/SeqIO/gcg.pm | 4 +-
Bio/SeqIO/genbank.pm | 12 +-
Bio/SeqIO/interpro.pm | 2 +-
Bio/SeqIO/lasergene.pm | 2 +-
Bio/SeqIO/mbsout.pm | 2 +-
Bio/SeqIO/msout.pm | 2 +-
Bio/SeqIO/pir.pm | 59 +-
Bio/SeqIO/seqxml.pm | 2 +-
Bio/SeqIO/swiss.pm | 4 +-
Bio/SeqIO/tigr.pm | 4 +-
Bio/SeqUtils.pm | 2 +-
Bio/Structure/Entry.pm | 4 +-
Bio/Structure/Residue.pm | 4 +-
Bio/Structure/SecStr/DSSP/Res.pm | 8 +-
Bio/Structure/SecStr/STRIDE/Res.pm | 2 +-
Bio/Taxonomy.pm | 4 +-
Bio/Tools/AlignFactory.pm | 26 +-
Bio/Tools/Analysis/DNA/ESEfinder.pm | 2 +-
Bio/Tools/Analysis/Protein/ELM.pm | 2 +-
Bio/Tools/Analysis/Protein/NetPhos.pm | 4 +-
Bio/Tools/ECnumber.pm | 2 +-
Bio/Tools/GFF.pm | 140 +-
Bio/Tools/Phylo/Gerp.pm | 2 +-
Bio/Tools/Phylo/PAML.pm | 1872 --------------------
Bio/Tools/Phylo/PAML/Codeml.pm | 255 ---
Bio/Tools/Phylo/PAML/ModelResult.pm | 564 ------
Bio/Tools/Phylo/PAML/Result.pm | 1238 -------------
Bio/Tools/PrositeScan.pm | 49 +-
Bio/Tools/SiRNA.pm | 2 +-
Bio/Tools/Sigcleave.pm | 2 +-
Bio/Tools/dpAlign.pm | 2 +-
Bio/Tools/pSW.pm | 4 +-
Bio/Tree/AlleleNode.pm | 2 +-
Bio/Tree/NodeI.pm | 2 +-
Bio/Tree/TreeFunctionsI.pm | 6 +-
Bio/TreeIO/nexus.pm | 2 +-
Bio/TreeIO/pag.pm | 2 +-
Bio/Variation/AAReverseMutate.pm | 2 +-
Bio/Variation/VariantI.pm | 6 +-
Changes | 21 +
DEPENDENCIES | 361 ++--
INSTALL.md | 81 +-
MANIFEST | 39 +-
META.json | 1619 +++++++++--------
META.yml | 1615 +++++++++--------
deobfuscator/Deobfuscator/bin/deob_index.pl | 30 +-
deobfuscator/Deobfuscator/cgi-bin/deob_detail.cgi | 2 +-
deobfuscator/Deobfuscator/cgi-bin/deob_help.html | 4 +-
.../Deobfuscator/cgi-bin/deob_interface.cgi | 4 +-
deobfuscator/Deobfuscator/lib/Deobfuscator.pm | 28 +-
examples/searchio/blast_example.pl | 4 +-
scripts/DB/bp_flanks.pl | 2 +-
scripts/index/bp_fetch.pl | 6 +-
scripts/index/bp_index.pl | 4 +-
scripts/seq/bp_seqcut.pl | 2 +-
scripts/seq/bp_unflatten_seq.pl | 2 +-
scripts/utilities/bp_netinstall.pl | 2 +-
scripts/utilities/bp_pairwise_kaks.pl | 211 ---
scripts/utilities/bp_search2gff.pl | 2 +-
t/LocalDB/Flat.t | 11 +-
t/RemoteDB/SeqVersion.t | 2 +-
t/RemoteDB/Taxonomy.t | 49 +-
t/SeqIO/pir.t | 48 +-
t/Tools/Phylo/PAML.t | 545 ------
t/Tools/PrositeScan.t | 44 +
t/data/M0.mlc | 159 --
t/data/aaml.mlc | 54 -
t/data/aaml_pairwise.mlc | 49 -
t/data/baseml.pairwise | 31 -
t/data/baseml.usertree | 42 -
t/data/branchSite.mlc | 115 --
t/data/bug3331.mlc | 128 --
t/data/codeml.mlc | 190 --
t/data/codeml315.mlc | 132 --
t/data/codeml4.mlc | 230 ---
t/data/codeml43.mlc | 231 ---
t/data/codeml43_nssites.mlc | 251 ---
t/data/codeml45.mlc | 460 -----
t/data/codeml_lysozyme/2NG.dN | 8 -
t/data/codeml_lysozyme/2NG.dS | 8 -
t/data/codeml_lysozyme/2NG.tt | 8 -
t/data/codeml_lysozyme/4fold.nuc | 26 -
t/data/codeml_lysozyme/lnf | 170 --
t/data/codeml_lysozyme/lysozymeSmall.ctl | 37 -
t/data/codeml_lysozyme/lysozymeSmall.trees | 36 -
t/data/codeml_lysozyme/lysozymeSmall.txt | 64 -
t/data/codeml_lysozyme/mlc | 273 ---
t/data/codeml_lysozyme/rst | 1165 ------------
t/data/codeml_lysozyme/rst1 | 1 -
t/data/codeml_lysozyme/rub | 48 -
t/data/codeml_nan.mlc | 177 --
t/data/codeml_nssites.mlc | 329 ----
t/data/ps_scan/out.PrositeScan | 10 +
t/data/seqfile-no-desc.pir | 9 +
t/data/singleNSsite.mlc | 152 --
t/data/testaln.xmfa | 14 +-
t/data/yn00.mlc | 106 --
t/data/yn00_45.mlc | 595 -------
travis_scripts/trigger-dockerhub.sh | 5 +
259 files changed, 3305 insertions(+), 12995 deletions(-)
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