| 2013-05-29 |
Sarah Westcott | get.seqs not renaming sequences correctly for dups...
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commit | commitdiff | tree |
| 2013-05-29 |
Sarah Westcott | added rename.seqs command.
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commit | commitdiff | tree |
| 2013-05-28 |
Sarah Westcott | case sensitive include statement caused issues for...
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commit | commitdiff | tree |
| 2013-05-28 |
Sarah Westcott | citation changes for 1.31.0
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commit | commitdiff | tree |
| 2013-05-24 |
Sarah Westcott | Merge remote-tracking branch 'origin'
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commit | commitdiff | tree |
| 2013-05-24 |
Sarah Westcott | added debugging to otu.association
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commit | commitdiff | tree |
| 2013-05-23 |
Sarah Westcott | changes while testing
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commit | commitdiff | tree |
| 2013-05-17 |
Sarah Westcott | changed how rarefaction commands find the lci and hci...
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commit | commitdiff | tree |
| 2013-05-17 |
Sarah Westcott | added modify names parameter to set.dir
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commit | commitdiff | tree |
| 2013-05-15 |
Sarah Westcott | added make.lookup command.
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commit | commitdiff | tree |
| 2013-05-14 |
Sarah Westcott | added count file to create.database command. corrected...
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commit | commitdiff | tree |
| 2013-05-13 |
Sarah Westcott | cluster.split was not sorting the list file in order...
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commit | commitdiff | tree |
| 2013-05-13 |
Sarah Westcott | added sparcc command. fixed bug in remove.groups that...
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commit | commitdiff | tree |
| 2013-05-06 |
Sarah Westcott | paralellized parsimony, unifrac.unweighted, phylo.diversity...
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commit | commitdiff | tree |
| 2013-02-13 |
Sarah Westcott | added trim overlap parameter to make.contigs
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commit | commitdiff | tree |
| 2013-02-13 |
Sarah Westcott | added merge.taxsummary command. added column format...
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commit | commitdiff | tree |
| 2013-02-12 |
Sarah Westcott | added order=A or order=B to trim.flows and shhh.flows...
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commit | commitdiff | tree |
| 2013-02-11 |
Sarah Westcott | added ':' name check to seq. error and fastq.info....
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commit | commitdiff | tree |
| 2013-02-06 |
Sarah Westcott | added *.count.summary file to count.groups command...
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commit | commitdiff | tree |
| 2013-01-29 |
Sarah Westcott | added get.dists and remove.dists commands. fixed bug...
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commit | commitdiff | tree |
| 2013-01-28 |
Sarah Westcott | added checks to make sure windows processes completed...
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commit | commitdiff | tree |
| 2013-01-25 |
Sarah Westcott | added primer.design command. fixed bug with linux...
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commit | commitdiff | tree |
| 2013-01-18 |
Sarah Westcott | fixed seq. error align=f issue. added std and ave calcs...
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commit | commitdiff | tree |
| 2013-01-16 |
Sarah Westcott | added topdown parameter to pre.cluster. added more...
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commit | commitdiff | tree |
| 2013-01-11 |
Sarah Westcott | fixed bug in pre.cluster with output file name change...
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commit | commitdiff | tree |
| 2013-01-08 |
Sarah Westcott | added dereplicate parameter to chimera.slayer and chimera...
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commit | commitdiff | tree |
| 2013-01-04 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2013-01-04 |
Sarah Westcott | added filter.shared command. fixed lci and uci for...
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commit | commitdiff | tree |
| 2012-12-21 |
Sarah Westcott | added ignore option to oligos files for make.contigs...
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commit | commitdiff | tree |
| 2012-12-21 |
Sarah Westcott | trim.seqs filename
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commit | commitdiff | tree |
| 2012-12-21 |
Sarah Westcott | working on make.contigs. fixed trim.seqs filename issue
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commit | commitdiff | tree |
| 2012-12-18 |
Sarah Westcott | added sharedotu parameter to venn command. working...
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commit | commitdiff | tree |
| 2012-12-17 |
Sarah Westcott | fixed issue in tree.shared when shared file was not...
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commit | commitdiff | tree |
| 2012-12-14 |
Sarah Westcott | added warning to readBlast to warn about duplicate...
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commit | commitdiff | tree |
| 2012-12-14 |
Sarah Westcott | added kruskwalliscommand to Xcode project and fixed...
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commit | commitdiff | tree |
| 2012-12-14 |
Sarah Westcott | fixed outputName creator, added debugging to readblast
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commit | commitdiff | tree |
| 2012-12-13 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-12-13 |
Sarah Westcott | fixed bug in phylo.diversity rooting. added filename...
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commit | commitdiff | tree |
| 2012-11-06 |
Sarah Westcott | changed added group output to indicator command. a...
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commit | commitdiff | tree |
| 2012-11-02 |
Sarah Westcott | fix to summary.tax for 1.28.0
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commit | commitdiff | tree |
| 2012-10-30 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-10-30 |
Sarah Westcott | classify.seqs allows sequences to be in taxonomy file...
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commit | commitdiff | tree |
| 2012-10-22 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-10-22 |
Sarah Westcott | added sets to amova and homova commands. added oligos...
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commit | commitdiff | tree |
| 2012-10-09 |
Sarah Westcott | changed dups parameter to dereplicate in chimera.uchime.
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commit | commitdiff | tree |
| 2012-10-09 |
Sarah Westcott | added dups parameter to chimera.uchime. working on...
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commit | commitdiff | tree |
| 2012-10-03 |
Sarah Westcott | added zap method to classify.seqs and changed bayesian...
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commit | commitdiff | tree |
| 2012-10-02 |
Sarah Westcott | added classify.shared command and random forest files...
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commit | commitdiff | tree |
| 2012-09-25 |
Sarah Westcott | added count file to get.oturep, pre.cluster, screen...
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commit | commitdiff | tree |
| 2012-09-14 |
Sarah Westcott | added count file to trim.seqs, get.groups, get.lineage...
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commit | commitdiff | tree |
| 2012-09-12 |
Sarah Westcott | optimizing classify.seqs calculating of template probabilities.
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commit | commitdiff | tree |
| 2012-09-11 |
Sarah Westcott | added count file to get.groups and remove.groups. added...
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commit | commitdiff | tree |
| 2012-09-07 |
Sarah Westcott | major change to the tree class to use the count table...
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commit | commitdiff | tree |
| 2012-08-24 |
Sarah Westcott | added sff.multiple command. fixed issue with windows...
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commit | commitdiff | tree |
| 2012-08-21 |
Sarah Westcott | added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs...
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commit | commitdiff | tree |
| 2012-08-14 |
Sarah Westcott | added code to format fast files for uchime. started...
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commit | commitdiff | tree |
| 2012-08-13 |
Sarah Westcott | added count file to chimera.uchime. found issue with...
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commit | commitdiff | tree |
| 2012-08-08 |
Sarah Westcott | added count parameter to chimera.slayer command
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commit | commitdiff | tree |
| 2012-08-08 |
Sarah Westcott | added SequenceCountParser class to parse the count...
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commit | commitdiff | tree |
| 2012-08-06 |
Sarah Westcott | changes while testing 1.27
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commit | commitdiff | tree |
| 2012-08-01 |
Sarah Westcott | paralellized chop.seqs
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commit | commitdiff | tree |
| 2012-07-31 |
Sarah Westcott | added count file to cluster.classic and cluster.split...
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commit | commitdiff | tree |
| 2012-07-30 |
Sarah Westcott | fixed subsample name file name issue. added count...
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commit | commitdiff | tree |
| 2012-07-27 |
Sarah Westcott | added sparseDistanceMatrix class. Modified cluster...
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commit | commitdiff | tree |
| 2012-07-11 |
Sarah Westcott | working on adding count file to mgcluster
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commit | commitdiff | tree |
| 2012-07-11 |
Sarah Westcott | working on mgcluster count file change
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commit | commitdiff | tree |
| 2012-07-11 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-07-11 |
Sarah Westcott | added debug statements to trim.seqs
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commit | commitdiff | tree |
| 2012-07-10 |
Sarah Westcott | changes while testing 1.26
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commit | commitdiff | tree |
| 2012-07-03 |
Sarah Westcott | changes while testing 1.26
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commit | commitdiff | tree |
| 2012-06-28 |
Sarah Westcott | added countable class to read and store count file...
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commit | commitdiff | tree |
| 2012-06-26 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-06-26 |
Sarah Westcott | made make.table alias to count.seqs command. added...
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commit | commitdiff | tree |
| 2012-06-19 |
Sarah Westcott | added phylip as output file type for commands that...
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commit | commitdiff | tree |
| 2012-06-19 |
Sarah Westcott | added load.logfile command. changed summary.single...
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commit | commitdiff | tree |
| 2012-06-12 |
Sarah Westcott | changed reading of name file to use buffered reads...
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commit | commitdiff | tree |
| 2012-06-11 |
Sarah Westcott | fixed bug with dist.shared subsampling. added mode...
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commit | commitdiff | tree |
| 2012-06-05 |
Sarah Westcott | added forward and reverse barcodes to trim.seqs to...
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commit | commitdiff | tree |
| 2012-06-04 |
Sarah Westcott | fixed classify.seqs output file name - had issue if...
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commit | commitdiff | tree |
| 2012-06-04 |
Sarah Westcott | added check to make sure shhh.flows child processes...
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commit | commitdiff | tree |
| 2012-05-29 |
Sarah Westcott | added code to check path for uchime and catchall executables
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commit | commitdiff | tree |
| 2012-05-24 |
Sarah Westcott | forced rarefaction.single to output ending line for...
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commit | commitdiff | tree |
| 2012-05-24 |
Sarah Westcott | fixed bug in sffinfo when ~ was used in the sff filename...
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commit | commitdiff | tree |
| 2012-05-23 |
Sarah Westcott | added metadata parameter to otu.association
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commit | commitdiff | tree |
| 2012-05-23 |
Sarah Westcott | added design and sets parameters to the rarefaction...
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commit | commitdiff | tree |
| 2012-05-22 |
Sarah Westcott | added debug output classify.seqs. worked on make.contigs...
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commit | commitdiff | tree |
| 2012-05-21 |
Sarah Westcott | added get.otulabels and remove.otulabels commands per...
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commit | commitdiff | tree |
| 2012-05-18 |
Sarah Westcott | added threshold parameter to make.contigs command.
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commit | commitdiff | tree |
| 2012-05-18 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-05-18 |
Sarah Westcott | added check to cluster.classic to make sure file type...
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commit | commitdiff | tree |
| 2012-05-16 |
Sarah Westcott | added classic parameter to cluster.split. working...
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commit | commitdiff | tree |
| 2012-05-15 |
Sarah Westcott | added list.labels command. started work on make.contigs...
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commit | commitdiff | tree |
| 2012-05-14 |
Sarah Westcott | last checkin for 1.25.1
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commit | commitdiff | tree |
| 2012-05-14 |
Sarah Westcott | fixed bug in make.biom that occurred if some taxonomies...
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commit | commitdiff | tree |
| 2012-05-14 |
Sarah Westcott | Merge remote-tracking branch 'origin/master'
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commit | commitdiff | tree |
| 2012-05-14 |
Sarah Westcott | added debug info to engines function to get mother...
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commit | commitdiff | tree |
| 2012-05-11 |
Sarah Westcott | added some debug stuff to chimera.uchime. optimized...
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commit | commitdiff | tree |
| 2012-05-11 |
Sarah Westcott | fixed path redirect issue in shhh.flows. optimized...
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commit | commitdiff | tree |
| 2012-05-10 |
Sarah Westcott | fixed typos
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commit | commitdiff | tree |
| 2012-05-10 |
Sarah Westcott | added abundance and sample parameters to get.coremicrobiome...
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commit | commitdiff | tree |
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