Public Git Hosting - bioperl-live.git/commit

commit	6506c2e4f2348a0377bbda1a39d9743fffb444e0
author	cjfields <cjfields@bioperl.org>
	Tue, 15 Sep 2009 21:57:56 +0000 (15 21:57 -0000)
committer	cjfields <cjfields@bioperl.org>
	Tue, 15 Sep 2009 21:57:56 +0000 (15 21:57 -0000)
tree	522608fdafcf73b77c7e865d3623d8d61944e619	tree \| snapshot (tar.gz zip)
parent	7ed0a02986d4f5768d3f4c3b1777edaa26b09804	commit \| diff

sync with trunk (to r15946)

svn path=/bioperl-live/branches/branch-1-6/; revision=16090

143 files changed:

AUTHORS		diff \| blob \| blame \| history
Bio/Align/AlignI.pm		diff \| blob \| blame \| history
Bio/Align/PairwiseStatistics.pm		diff \| blob \| blame \| history
Bio/AlignIO/arp.pm		diff \| blob \| blame \| history
Bio/AlignIO/clustalw.pm		diff \| blob \| blame \| history
Bio/AlignIO/fasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/largemultifasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/maf.pm		diff \| blob \| blame \| history
Bio/AlignIO/mase.pm		diff \| blob \| blame \| history
Bio/AlignIO/mega.pm		diff \| blob \| blame \| history
Bio/AlignIO/metafasta.pm		diff \| blob \| blame \| history
Bio/AlignIO/msf.pm		diff \| blob \| blame \| history
Bio/AlignIO/nexus.pm		diff \| blob \| blame \| history
Bio/AlignIO/pfam.pm		diff \| blob \| blame \| history
Bio/AlignIO/phylip.pm		diff \| blob \| blame \| history
Bio/AlignIO/po.pm		diff \| blob \| blame \| history
Bio/AlignIO/proda.pm		diff \| blob \| blame \| history
Bio/AlignIO/prodom.pm		diff \| blob \| blame \| history
Bio/AlignIO/psi.pm		diff \| blob \| blame \| history
Bio/AlignIO/selex.pm		diff \| blob \| blame \| history
Bio/AlignIO/stockholm.pm		diff \| blob \| blame \| history
Bio/AlignIO/xmfa.pm		diff \| blob \| blame \| history
Bio/Assembly/Contig.pm		diff \| blob \| blame \| history
Bio/Assembly/IO/tigr.pm		diff \| blob \| blame \| history
Bio/Assembly/Tools/ContigSpectrum.pm		diff \| blob \| blame \| history
Bio/DB/HIV/lanl-schema.xml		diff \| blob \| blame \| history
Bio/DB/Query/GenBank.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/DBI/SQLite.pm	[new file with mode: 0644]	blob
Bio/DB/SeqFeature/Store/DBI/mysql.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/GFF3Loader.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/berkeleydb.pm		diff \| blob \| blame \| history
Bio/PopGen/GenotypeI.pm		diff \| blob \| blame \| history
Bio/PopGen/Individual.pm		diff \| blob \| blame \| history
Bio/PopGen/IndividualI.pm		diff \| blob \| blame \| history
Bio/PopGen/Marker.pm		diff \| blob \| blame \| history
Bio/PopGen/MarkerI.pm		diff \| blob \| blame \| history
Bio/PopGen/Population.pm		diff \| blob \| blame \| history
Bio/PopGen/PopulationI.pm		diff \| blob \| blame \| history
Bio/PrimarySeq.pm		diff \| blob \| blame \| history
Bio/Restriction/Analysis.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme/MultiCut.pm		diff \| blob \| blame \| history
Bio/Restriction/Enzyme/MultiSite.pm		diff \| blob \| blame \| history
Bio/Restriction/EnzymeCollection.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/base.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/itype2.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/prototype.pm		diff \| blob \| blame \| history
Bio/Restriction/IO/withrefm.pm		diff \| blob \| blame \| history
Bio/Root/Build.pm		diff \| blob \| blame \| history
Bio/Root/IO.pm		diff \| blob \| blame \| history
Bio/Root/Root.pm		diff \| blob \| blame \| history
Bio/Root/RootI.pm		diff \| blob \| blame \| history
Bio/Search/HSP/HSPI.pm		diff \| blob \| blame \| history
Bio/Search/HSP/ModelHSP.pm		diff \| blob \| blame \| history
Bio/Search/Hit/GenericHit.pm		diff \| blob \| blame \| history
Bio/Search/Hit/ModelHit.pm		diff \| blob \| blame \| history
Bio/Search/SearchUtils.pm		diff \| blob \| blame \| history
Bio/Search/Tiling/MapTileUtils.pm	[new file with mode: 0755]	blob
Bio/Search/Tiling/MapTiling.pm	[new file with mode: 0755]	blob
Bio/Search/Tiling/TilingI.pm	[new file with mode: 0755]	blob
Bio/SearchIO/exonerate.pm		diff \| blob \| blame \| history
Bio/SearchIO/fasta.pm		diff \| blob \| blame \| history
Bio/SearchIO/infernal.pm		diff \| blob \| blame \| history
Bio/SearchIO/psl.pm		diff \| blob \| blame \| history
Bio/Seq/Quality.pm		diff \| blob \| blame \| history
Bio/SeqFeature/Lite.pm		diff \| blob \| blame \| history
Bio/SeqIO.pm		diff \| blob \| blame \| history
Bio/SeqIO/fasta.pm		diff \| blob \| blame \| history
Bio/SeqIO/fastq.pm		diff \| blob \| blame \| history
Bio/SeqIO/raw.pm		diff \| blob \| blame \| history
Bio/SeqIO/scf.pm		diff \| blob \| blame \| history
Bio/SimpleAlign.pm		diff \| blob \| blame \| history
Bio/Tools/CodonTable.pm		diff \| blob \| blame \| history
Bio/Tools/EUtilities/Link/LinkSet.pm		diff \| blob \| blame \| history
Bio/Tools/EUtilities/Summary/DocSum.pm		diff \| blob \| blame \| history
Bio/Tools/EUtilities/Summary/Item.pm		diff \| blob \| blame \| history
Bio/Tools/EUtilities/Summary/ItemContainerI.pm	[copied from Bio/Tools/EUtilities/Summary/DocSum.pm with 65% similarity]	diff \| blob \| blame \| history
Bio/Tools/HMM.pm		diff \| blob \| blame \| history
Bio/Tools/Primer3.pm		diff \| blob \| blame \| history
Bio/Tools/Run/RemoteBlast.pm		diff \| blob \| blame \| history
Bio/Tools/Run/WrapperBase.pm		diff \| blob \| blame \| history
Bio/Tools/SeqPattern.pm		diff \| blob \| blame \| history
Bio/Tools/SeqPattern/Backtranslate.pm	[new file with mode: 0644]	blob
Bio/Tree/Tree.pm		diff \| blob \| blame \| history
Bio/Tree/TreeFunctionsI.pm		diff \| blob \| blame \| history
Bio/TreeIO.pm		diff \| blob \| blame \| history
Build.PL		diff \| blob \| blame \| history
PLATFORMS	[deleted file]	blob \| blame \| history
scripts/DB-HIV/hivq.PLS		diff \| blob \| blame \| history
t/Align/SimpleAlign.t		diff \| blob \| blame \| history
t/Align/Utilities.t		diff \| blob \| blame \| history
t/AlignIO/AlignIO.t		diff \| blob \| blame \| history
t/AlignIO/arp.t		diff \| blob \| blame \| history
t/AlignIO/meme.t		diff \| blob \| blame \| history
t/AlignIO/po.t		diff \| blob \| blame \| history
t/AlignIO/psi.t		diff \| blob \| blame \| history
t/LocalDB/transfac_pro.t		diff \| blob \| blame \| history
t/RemoteDB/HIV/HIVQueryHelper.t		diff \| blob \| blame \| history
t/Restriction/Analysis-refac.t	[new file with mode: 0755]	blob
t/Root/RootI.t		diff \| blob \| blame \| history
t/SearchIO/Tiling.t	[new file with mode: 0755]	blob
t/SearchIO/blast.t		diff \| blob \| blame \| history
t/SearchIO/exonerate.t		diff \| blob \| blame \| history
t/SearchIO/infernal.t		diff \| blob \| blame \| history
t/SearchIO/psl.t		diff \| blob \| blame \| history
t/Seq/LocatableSeq.t		diff \| blob \| blame \| history
t/Seq/PrimarySeq.t		diff \| blob \| blame \| history
t/Seq/Seq.t		diff \| blob \| blame \| history
t/SeqIO/fasta.t		diff \| blob \| blame \| history
t/SeqIO/fastq.t		diff \| blob \| blame \| history
t/SeqIO/raw.t		diff \| blob \| blame \| history
t/SeqIO/scf.t		diff \| blob \| blame \| history
t/SeqTools/Backtranslate.t	[new file with mode: 0644]	blob
t/SeqTools/SeqPattern.t		diff \| blob \| blame \| history
t/SeqTools/SeqUtils.t		diff \| blob \| blame \| history
t/Tools/EUtilities/esummary.t		diff \| blob \| blame \| history
t/Tools/Primer3.t		diff \| blob \| blame \| history
t/Tools/Run/RemoteBlast_rpsblast.t	[new file with mode: 0644]	blob
t/Tree/Node.t		diff \| blob \| blame \| history
t/bugzilla/2346/exonerate.output.dontwork	[new file with mode: 0644]	blob
t/bugzilla/2346/exonerate.output.works	[new file with mode: 0644]	blob
t/bugzilla/2346/in.t	[new file with mode: 0644]	blob
t/bugzilla/2537/in.fasta	[new file with mode: 0644]	blob
t/bugzilla/2537/in.t	[new file with mode: 0644]	blob
t/bugzilla/2842/mask.t	[new file with mode: 0644]	blob
t/bugzilla/2844/note.txt	[new file with mode: 0644]	blob
t/bugzilla/2847/bug.t	[new file with mode: 0644]	blob
t/bugzilla/2847/test_clear_range.fastq	[new file with mode: 0644]	blob
t/bugzilla/2850/bug.t	[new file with mode: 0644]	blob
t/bugzilla/2850/headerless.psl	[new file with mode: 0644]	blob
t/bugzilla/README	[new file with mode: 0644]	blob
t/data/1ZZ19XR301R-Alignment.tblastn	[new file with mode: 0755]	blob
t/data/bug2862.pmr	[new file with mode: 0644]	blob
t/data/contig-by-hand.wublastp	[new file with mode: 0755]	blob
t/data/fastq/bug2335.fastq	[moved from t/data/bug2335.fastq with 100% similarity]	blob \| blame \| history
t/data/fastq/test1_sanger.fastq	[new file with mode: 0644]	blob
t/data/fastq/test2_solexa.fastq	[new file with mode: 0644]	blob
t/data/fastq/test3_illumina.fastq	[new file with mode: 0644]	blob
t/data/frac_problems2.blast		diff \| blob \| blame \| history
t/data/test2.infernal	[new file with mode: 0644]	blob
t/data/test2.raw	[new file with mode: 0644]	blob
t/data/withrefm.906	[new file with mode: 0755]	blob

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