[Bioperl-l] Extremely Bad News for 0.6.2 release

Peter van Heusden pvh@egenetics.com
Wed, 30 Aug 2000 13:38:18 +0200 (SAST)


Some very bad news.... turns out I need to learn a bit more about CVS. Due
to 'sticky' tags, I didn't get all the info on differences between
branch-06 and the head of the CVS trunk. The result? My initial estimate
of 2225 lines of diffs is now revised to 23113 lines of diffs, covering
183 out of 307 files in the BioPerl tree.

So - where to from here? I'm going to go through another process of
deciding which changes are significant, but it would be useful if
volunteers could step forward so that I could spread the workload. Can
anyone who has time to write up the significance of changes in a
particular branch of the tree please contact me?

Thanks,
Peter

P.S. Here's a list of changed files, with a count of lines of diff...

Index: bioperl-live/Changes 59
Index: bioperl-live/MANIFEST 104
Index: bioperl-live/MANIFEST.SKIP 9
Index: bioperl-live/PLATFORMS 80
Index: bioperl-live/README 96
Index: bioperl-live/biodesign.pod 60
Index: bioperl-live/bioperl.pod 37
Index: bioperl-live/Bio/Annotation.pm 115
Index: bioperl-live/Bio/DBLinkContainerI.pm 124
Index: bioperl-live/Bio/LocatableSeq.pm 57
Index: bioperl-live/Bio/PrimarySeq.pm 45
Index: bioperl-live/Bio/PrimarySeqI.pm 116
Index: bioperl-live/Bio/Seq.pm 153
Index: bioperl-live/Bio/SeqFeatureI.pm 93
Index: bioperl-live/Bio/SeqFeatureProducerI.pm 109
Index: bioperl-live/Bio/SeqI.pm 28
Index: bioperl-live/Bio/SeqIO.pm 335
Index: bioperl-live/Bio/SimpleAlign.pm 33
Index: bioperl-live/Bio/UnivAln.pm 40
Index: bioperl-live/Bio/Annotation/Comment.pm 48
Index: bioperl-live/Bio/Annotation/DBLink.pm 102
Index: bioperl-live/Bio/Annotation/Reference.pm 189
Index: bioperl-live/Bio/DB/Ace.pm 32
Index: bioperl-live/Bio/DB/GenBank.pm 198
Index: bioperl-live/Bio/DB/GenPept.pm 186
Index: bioperl-live/Bio/DB/RandomAccessI.pm 11
Index: bioperl-live/Bio/DB/SeqI.pm 19
Index: bioperl-live/Bio/DB/UpdateableSeqI.pm 235
Index: bioperl-live/Bio/Index/Abstract.pm 24
Index: bioperl-live/Bio/Index/AbstractSeq.pm 65
Index: bioperl-live/Bio/Index/EMBL.pm 25
Index: bioperl-live/Bio/Index/Fasta.pm 47
Index: bioperl-live/Bio/Index/GenBank.pm 234
Index: bioperl-live/Bio/Index/SwissPfam.pm 24
Index: bioperl-live/Bio/Index/Swissprot.pm 237
Index: bioperl-live/Bio/Root/Err.pm 34
Index: bioperl-live/Bio/Root/Global.pm 22
Index: bioperl-live/Bio/Root/IOManager.pm 25
Index: bioperl-live/Bio/Root/Object.pm 125
Index: bioperl-live/Bio/Root/RootI.pm 100
Index: bioperl-live/Bio/Root/Utilities.pm 51
Index: bioperl-live/Bio/Root/Vector.pm 25
Index: bioperl-live/Bio/Root/Xref.pm 25
Index: bioperl-live/Bio/SeqFeature/FeaturePair.pm 68
Index: bioperl-live/Bio/SeqFeature/GeneStructure.pm 668
Index: bioperl-live/Bio/SeqFeature/Generic.pm 195
Index: bioperl-live/Bio/SeqFeature/Similarity.pm 217
Index: bioperl-live/Bio/SeqFeature/SimilarityPair.pm 388
Index: bioperl-live/Bio/SeqFeatureProducer/GFF.pm 149
Index: bioperl-live/Bio/SeqFeatureProducer/MZEF.pm 168
Index: bioperl-live/Bio/SeqIO/GAMEHandler.pm 266
Index: bioperl-live/Bio/SeqIO/ace.pm 217
Index: bioperl-live/Bio/SeqIO/bioxml.pm 225
Index: bioperl-live/Bio/SeqIO/embl.pm 54
Index: bioperl-live/Bio/SeqIO/fasta.pm 19
Index: bioperl-live/Bio/SeqIO/gcg.pm 29
Index: bioperl-live/Bio/SeqIO/genbank.pm 383
Index: bioperl-live/Bio/SeqIO/pir.pm 20
Index: bioperl-live/Bio/SeqIO/swiss.pm 486
Index: bioperl-live/Bio/Tools/BPlite.pm 288
Index: bioperl-live/Bio/Tools/Blast.pm 70
Index: bioperl-live/Bio/Tools/CodonTable.pm 38
Index: bioperl-live/Bio/Tools/Genscan.pm 499
Index: bioperl-live/Bio/Tools/MZEF.pm 408
Index: bioperl-live/Bio/Tools/OddCodes.pm 446
Index: bioperl-live/Bio/Tools/RestrictionEnzyme.pm 103
Index: bioperl-live/Bio/Tools/SeqPattern.pm 162
Index: bioperl-live/Bio/Tools/SeqStats.pm 87
Index: bioperl-live/Bio/Tools/SeqWords.pm 145
Index: bioperl-live/Bio/Tools/pSW.pm 69
Index: bioperl-live/Bio/Tools/BPlite/HSP.pm 113
Index: bioperl-live/Bio/Tools/BPlite/Sbjct.pm 146
Index: bioperl-live/Bio/Tools/Blast/HSP.pm 35
Index: bioperl-live/Bio/Tools/Blast/HTML.pm 21
Index: bioperl-live/Bio/Tools/Blast/Sbjct.pm 21
Index: bioperl-live/Bio/Tools/Blast/Run/LocalBlast.pm 21
Index: bioperl-live/Bio/Tools/Blast/Run/Webblast.pm 12
Index: bioperl-live/Bio/Tools/PPSEARCH/Parse.pm 154
Index: bioperl-live/Bio/Tools/PRFSCAN/Parse.pm 143
Index: bioperl-live/Bio/Tools/PRINTS/Parse.pm 191
Index: bioperl-live/Bio/Tools/Prediction/Exon.pm 199
Index: bioperl-live/Bio/Tools/Prediction/Gene.pm 170
Index: bioperl-live/Bio/Tools/Sim4/Exon.pm 115
Index: bioperl-live/Bio/Tools/Sim4/ExonSet.pm 172
Index: bioperl-live/Bio/Tools/Sim4/Results.pm 587
Index: bioperl-live/Bio/Variation/AAChange.pm 378
Index: bioperl-live/Bio/Variation/AAReverseMutate.pm 310
Index: bioperl-live/Bio/Variation/Allele.pm 266
Index: bioperl-live/Bio/Variation/DNAMutation.pm 398
Index: bioperl-live/Bio/Variation/IO.pm 362
Index: bioperl-live/Bio/Variation/README 35
Index: bioperl-live/Bio/Variation/RNAChange.pm 642
Index: bioperl-live/Bio/Variation/SeqDiff.pm 996
Index: bioperl-live/Bio/Variation/VariantI.pm 1016
Index: bioperl-live/Bio/Variation/IO/flat.pm 759
Index: bioperl-live/Bio/Variation/IO/xml.pm 595
Index: bioperl-live/examples/gsequence 1629
Index: bioperl-live/examples/restriction.pl 12
Index: bioperl-live/examples/test-genscan.pl 75
Index: bioperl-live/examples/blast/blast_config.pl 12
Index: bioperl-live/examples/blast/blast_seq.pl 12
Index: bioperl-live/examples/blast/parse_positions.pl 22
Index: bioperl-live/examples/blast/print_blasts.pl 12
Index: bioperl-live/examples/blast/run_blast_remote.pl 12
Index: bioperl-live/scripts/blast_fetch.pl 25
Index: bioperl-live/scripts/bpfetch.pl 34
Index: bioperl-live/scripts/bpindex.pl 37
Index: bioperl-live/t/AAChange.t 216
Index: bioperl-live/t/AAReverseMutate.t 133
Index: bioperl-live/t/Allele.t 105
Index: bioperl-live/t/Annotation.t 81
Index: bioperl-live/t/BPlite.t 94
Index: bioperl-live/t/DNAMutation.t 247
Index: bioperl-live/t/HUMBETGLOA.fasta 56
Index: bioperl-live/t/HUMBETGLOA.gff 11
Index: bioperl-live/t/HUMBETGLOA.mzef 16
Index: bioperl-live/t/Index.t 12
Index: bioperl-live/t/PrimarySeq.t 43
Index: bioperl-live/t/RNAChange.t 260
Index: bioperl-live/t/Range.t 25
Index: bioperl-live/t/RestrictionEnzyme.t 47
Index: bioperl-live/t/Seq.t 10
Index: bioperl-live/t/SeqDiff.t 160
Index: bioperl-live/t/SeqFeature.t 88
Index: bioperl-live/t/SeqFeatureProducer.t 108
Index: bioperl-live/t/SeqIO.t 386
Index: bioperl-live/t/SimpleAlign.t 30
Index: bioperl-live/t/Species.t 10
Index: bioperl-live/t/Tools.t 35
Index: bioperl-live/t/Variation_IO.t 188
Index: bioperl-live/t/mutations.dat 256
Index: bioperl-live/t/mutations.xml 278
Index: bioperl-live/t/polymorphism.dat 78
Index: bioperl-live/t/polymorphism.xml 85
Index: bioperl-live/t/seq.xml 36
Index: bioperl-live/t/test.ace 37
Index: bioperl-live/t/test.embl 240
Index: bioperl-live/t/test.genbank 213

_______________/\/eGenetics.com\/\_______________
Peter van Heusden				pvh@egenetics.com
Electric Genetics