From 97074c7844a9e9aec48c2a5c7fca31a5bdb89e54 Mon Sep 17 00:00:00 2001 From: Chris Fields Date: Thu, 17 Mar 2011 10:36:38 -0500 Subject: [PATCH] update manifest --- MANIFEST | 23 +++++++++++++++++++++-- 1 file changed, 21 insertions(+), 2 deletions(-) diff --git a/MANIFEST b/MANIFEST index b2e5b8071..e79f1447d 100644 --- a/MANIFEST +++ b/MANIFEST @@ -1,4 +1,3 @@ -.shipit AUTHORS Bio/Align/AlignI.pm Bio/Align/DNAStatistics.pm @@ -547,6 +546,7 @@ Bio/SearchIO/fasta.pm Bio/SearchIO/FastHitEventBuilder.pm Bio/SearchIO/gmap_f9.pm Bio/SearchIO/hmmer.pm +Bio/SearchIO/hmmer2.pm Bio/SearchIO/hmmer3.pm Bio/SearchIO/hmmer_pull.pm Bio/SearchIO/infernal.pm @@ -852,6 +852,7 @@ Bio/TreeIO.pm Bio/TreeIO/cluster.pm Bio/TreeIO/lintree.pm Bio/TreeIO/newick.pm +Bio/TreeIO/NewickParser.pm Bio/TreeIO/nexml.pm Bio/TreeIO/nexus.pm Bio/TreeIO/nhx.pm @@ -1161,6 +1162,7 @@ t/data/503384.MEGABLAST.0 t/data/503384.MEGABLAST.2 t/data/5X_1895.FASTXY t/data/8HVP.pdb +t/data/9K_v4.psl t/data/a_thaliana.blastn t/data/AAC12660.fa t/data/aaml.mlc @@ -1200,6 +1202,7 @@ t/data/biodbgff/test.gff t/data/biodbgff/test.gff3 t/data/biofpc.cor t/data/biofpc.fpc +t/data/biorecipe.nhx t/data/Bird_Ovomucoids.nex t/data/BK000016-tpa.gbk t/data/bl2seq.blastn @@ -1383,10 +1386,12 @@ t/data/eutils/esearch2.xml t/data/eutils/espell.xml t/data/eutils/esummary1.xml t/data/eutils/esummary2.xml +t/data/ex1.nucl.nhx t/data/example.hap t/data/example.phase t/data/exonerate.output.dontwork t/data/exonerate.output.works +t/data/exonerate.whitespace_before_query.works t/data/expected.blast.out t/data/exsignalp.out t/data/factor7.embl @@ -1429,6 +1434,8 @@ t/data/fastq/test3_illumina.fastq t/data/fastq/tricky.fastq t/data/fastq/wrapping_issues.fastq t/data/fgenesh.out +t/data/fishBlats.txt +t/data/fishBlats_UCSC.psl t/data/footprinter.out t/data/frac_problems.blast t/data/frac_problems2.blast @@ -1465,6 +1472,7 @@ t/data/hmmpfam_cs.out t/data/hmmpfam_fake.out t/data/hmmscan.out t/data/hmmscan_multi_domain.out +t/data/hmmscan_sec_struct.out t/data/hmmsearch.out t/data/hmmsearch3.out t/data/hs_est.est2genome @@ -1488,6 +1496,7 @@ t/data/in.fasta t/data/insulin.water t/data/interpro.xml t/data/interpro_ebi.xml +t/data/interpro_relationship.xml t/data/interpro_sample.xml t/data/interpro_short.xml t/data/intrablock-comment.nex @@ -1629,6 +1638,7 @@ t/data/nei_gojobori_test.aln t/data/neighbor.dist t/data/new_blastn.txt t/data/newblast.xml +t/data/nhx-bacteria.nhx t/data/NM_002254.gb t/data/no-genes.genscan t/data/no_cds_example.gb @@ -1639,6 +1649,8 @@ t/data/noninterleaved.phy t/data/NT_021877.gbk t/data/nucmatrix.txt t/data/O_sat.wgs +t/data/O_ZNF496.blast +t/data/O_ZNF496.psl t/data/omim_genemap_test t/data/omim_genemap_test_nolinebreak t/data/omim_text_test @@ -1730,6 +1742,7 @@ t/data/singleNSsite.mlc t/data/singlet_w_CT.ace t/data/so.obo t/data/sofa.ontology +t/data/sp_subset.obo t/data/spaces.nex t/data/SPAN_Family4nl.nex t/data/SPAN_Family7n.nex @@ -1808,6 +1821,7 @@ t/data/test2.infernal t/data/test2.raw t/data/test_badlf.gcg t/data/test_clear_range.fastq +t/data/test_data.axt t/data/test_singlets.cns.fastq t/data/test_singlets.maq t/data/testaln.aln @@ -1836,6 +1850,7 @@ t/data/testfile.erpin t/data/testfuzzy.genbank t/data/tmhmm.out t/data/tmp.fst +t/data/tol-2010-02-18.nhx t/data/traits.tab t/data/traittree.nexus t/data/transfac.dat @@ -1857,12 +1872,14 @@ t/data/U71225.gb t/data/U71225.gb.unix t/data/U71225.gb.win t/data/U83300.bsml +t/data/UCSC_fishBlats.txt t/data/UnaSmithHIV-both.nex t/data/unigene.data t/data/urease.tre.nexus t/data/vecscreen_simple.test_output t/data/version2.scf t/data/version3.scf +t/data/wellcome_tol.nhx t/data/withrefm.906 t/data/worm_fam_2785.cdna t/data/X98338_Adh-mRNA.gb @@ -1977,6 +1994,7 @@ t/Root/Storable.t t/Root/Tempfile.t t/Root/Utilities.t t/SearchDist.t +t/SearchIO/axt.t t/SearchIO/blast.t t/SearchIO/blast_pull.t t/SearchIO/blasttable.t @@ -2003,6 +2021,7 @@ t/SearchIO/Writer/GbrowseGFF.t t/SearchIO/Writer/HitTableWriter.t t/SearchIO/Writer/HSPTableWriter.t t/SearchIO/Writer/HTMLWriter.t +t/SearchIO/Writer/TextWriter.t t/Seq/DBLink.t t/Seq/EncodedSeq.t t/Seq/LargeLocatableSeq.t @@ -2030,7 +2049,6 @@ t/SeqFeature/SeqFeature.t t/SeqFeature/SeqFeaturePrimer.t t/SeqFeature/Unflattener.t t/SeqFeature/Unflattener2.t -t/SeqIO.t t/SeqIO/abi.t t/SeqIO/ace.t t/SeqIO/agave.t @@ -2072,6 +2090,7 @@ t/SeqIO/qual.t t/SeqIO/raw.t t/SeqIO/scf.t t/SeqIO/SeqBuilder.t +t/SeqIO/SeqIO.t t/SeqIO/seqxml.t t/SeqIO/Splicedseq.t t/SeqIO/strider.t -- 2.11.4.GIT