Public Git Hosting - bioperl-live.git/commit

commit	fe3cba635c0c92e1d240d3f1cb98dad78700ff7f
author	cjfields <cjfields@bioperl.org>
	Tue, 15 Sep 2009 22:11:15 +0000 (15 22:11 -0000)
committer	cjfields <cjfields@bioperl.org>
	Tue, 15 Sep 2009 22:11:15 +0000 (15 22:11 -0000)
tree	f70d1ef5d03e4e362d7e4056fd8661c9b271f6e8	tree \| snapshot (tar.gz zip)
parent	6506c2e4f2348a0377bbda1a39d9743fffb444e0	commit \| diff

sync with main trunk completely (a few tests failing)

svn path=/bioperl-live/branches/branch-1-6/; revision=16091

77 files changed:

AUTHORS		diff \| blob \| blame \| history
Bio/DB/HIV.pm		diff \| blob \| blame \| history
Bio/DB/Query/HIVQuery.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/DBI/Pg.pm	[new file with mode: 0644]	blob
Bio/DB/SeqFeature/Store/DBI/SQLite.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/Loader.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/berkeleydb.pm		diff \| blob \| blame \| history
Bio/DB/SeqFeature/Store/berkeleydb3.pm	[new file with mode: 0644]	blob
Bio/Index/Fasta.pm		diff \| blob \| blame \| history
Bio/LocatableSeq.pm		diff \| blob \| blame \| history
Bio/Root/Test.pm		diff \| blob \| blame \| history
Bio/Search/HSP/FastaHSP.pm		diff \| blob \| blame \| history
Bio/SearchIO/gmap_f9.pm	[new file with mode: 0644]	blob
Bio/Seq/Meta/Array.pm		diff \| blob \| blame \| history
Bio/SeqFeature/Generic.pm		diff \| blob \| blame \| history
Bio/SeqFeature/Tools/TypeMapper.pm		diff \| blob \| blame \| history
Bio/SeqIO/fastq.pm		diff \| blob \| blame \| history
Bio/SeqIO/largefasta.pm		diff \| blob \| blame \| history
Bio/SeqIO/raw.pm		diff \| blob \| blame \| history
Bio/SimpleAlign.pm		diff \| blob \| blame \| history
Bio/Tools/HMM.pm	[deleted file]	blob \| blame \| history
Bio/Tools/dpAlign.pm		diff \| blob \| blame \| history
Bio/Tree/TreeFunctionsI.pm		diff \| blob \| blame \| history
Changes		diff \| blob \| blame \| history
bioperl.lisp		diff \| blob \| blame \| history
maintenance/perltidy.conf	[new file with mode: 0644]	blob
scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS		diff \| blob \| blame \| history
t/Align/SimpleAlign.t		diff \| blob \| blame \| history
t/LocalDB/SeqFeature.t		diff \| blob \| blame \| history
t/RemoteDB/BioFetch.t		diff \| blob \| blame \| history
t/RemoteDB/EMBL.t		diff \| blob \| blame \| history
t/RemoteDB/EUtilities.t		diff \| blob \| blame \| history
t/RemoteDB/SwissProt.t		diff \| blob \| blame \| history
t/Seq/EncodedSeq.t		diff \| blob \| blame \| history
t/Seq/LocatableSeq.t		diff \| blob \| blame \| history
t/SeqIO/fastq.t		diff \| blob \| blame \| history
t/SeqIO/raw.t		diff \| blob \| blame \| history
t/Tools/Primer3.t		diff \| blob \| blame \| history
t/data/bug2862.pmr		diff \| blob \| blame \| history
t/data/fastq/error_diff_ids.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_double_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_double_seq.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_long_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_no_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_del.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_escape.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_null.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_space.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_tab.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_unit_sep.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_qual_vtab.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_short_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_spaces.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_tabs.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_at_plus.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_at_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_at_seq.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_in_plus.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_in_qual.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_in_seq.fastq	[new file with mode: 0644]	blob
t/data/fastq/error_trunc_in_title.fastq	[new file with mode: 0644]	blob
t/data/fastq/evil_wrapping.fastq	[new file with mode: 0644]	blob
t/data/fastq/example.fasta	[new file with mode: 0644]	blob
t/data/fastq/example.fastq	[new file with mode: 0644]	blob
t/data/fastq/example.qual	[new file with mode: 0644]	blob
t/data/fastq/illumina_faked.fastq	[new file with mode: 0644]	blob
t/data/fastq/sanger_93.fastq	[new file with mode: 0644]	blob
t/data/fastq/sanger_faked.fastq	[new file with mode: 0644]	blob
t/data/fastq/solexa_example.fastq	[new file with mode: 0644]	blob
t/data/fastq/solexa_faked.fastq	[new file with mode: 0644]	blob
t/data/fastq/tricky.fastq	[new file with mode: 0644]	blob
t/data/fastq/wrapping_issues.fastq	[new file with mode: 0644]	blob
t/data/gmap_f9-multiple_results.txt	[new file with mode: 0644]	blob
t/data/gmap_f9-reverse-strand.txt	[new file with mode: 0644]	blob
t/data/gmap_f9.txt	[new file with mode: 0644]	blob
t/gmap_f9-searchio.t	[new file with mode: 0644]	blob

BioPerl core

RSS Atom