| 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 |
| 2012-05-09 |
Sarah Westcott | working on get.coremicrobiom
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commit | commitdiff | tree |
| 2012-05-09 |
Sarah Westcott | cluster.split split method defaults to classify if...
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | fixed segfault in unifrac with subsample. in progress...
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | Revert to previous commit
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | fixing
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | moving source to source folder
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | moved mothur's source into a folder to make grabbing...
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | removing chime source files from mother project.
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | another test
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | test2
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commit | commitdiff | tree |
| 2012-05-02 |
Sarah Westcott | test commit
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commit | commitdiff | tree |
| 2012-05-01 |
Sarah Westcott | Merge remote-tracking branch 'mothur/master'
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commit | commitdiff | tree |
| 2012-05-01 |
Sarah Westcott | bug in dist.shared and tree.shared with new subsampling...
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commit | commitdiff | tree |
| 2012-05-01 |
Sarah Westcott | changes while testing
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commit | commitdiff | tree |
| 2012-05-01 |
Sarah Westcott | Merge remote-tracking branch 'mothur/master'
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commit | commitdiff | tree |
| 2012-05-01 |
Sarah Westcott | fixed bug in rarefaction.single creating the groups...
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commit | commitdiff | tree |
| 2012-04-30 |
Sarah Westcott | changes while testing
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commit | commitdiff | tree |
| 2012-04-30 |
Sarah Westcott | Merge remote-tracking branch 'mothur/master'
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commit | commitdiff | tree |
| 2012-04-30 |
Sarah Westcott | changes while testing
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commit | commitdiff | tree |
| 2012-04-27 |
Sarah Westcott | Merge remote-tracking branch 'mothur/master'
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commit | commitdiff | tree |
| 2012-04-27 |
Sarah Westcott | changes while testing.
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commit | commitdiff | tree |
| 2012-04-23 |
Sarah Westcott | bugs found while testing
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commit | commitdiff | tree |
| 2012-04-23 |
Sarah Westcott | added check for positive values in pairwise.seqs gap...
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commit | commitdiff | tree |
| 2012-04-20 |
Sarah Westcott | added uchime_src folder. added biom parameter to make...
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commit | commitdiff | tree |
| 2012-04-17 |
Sarah Westcott | added make.biom command
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commit | commitdiff | tree |
| 2012-04-16 |
Sarah Westcott | added subsample and consensus parameters to unifrac...
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commit | commitdiff | tree |
| 2012-04-13 |
Sarah Westcott | fixing out labels to match those in shared file. If...
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commit | commitdiff | tree |
| 2012-04-13 |
Sarah Westcott | added tree reader class to handle reading trees. Reworked...
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commit | commitdiff | tree |
| 2012-04-11 |
Sarah Westcott | fixed bug with windows version of trim.seqs when run...
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commit | commitdiff | tree |
| 2012-04-11 |
Sarah Westcott | added subsample and consensus parameters to unifrac...
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commit | commitdiff | tree |
| 2012-04-05 |
Sarah Westcott | adding uchime source
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commit | commitdiff | tree |
| 2012-04-05 |
Sarah Westcott | deleted consensus command
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commit | commitdiff | tree |
| 2012-04-05 |
Sarah Westcott | added subsample, tiers and processors to tree.shared...
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commit | commitdiff | tree |
| 2012-04-03 |
Sarah Westcott | fixed bug in corr.axes so that it now uses the shared...
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commit | commitdiff | tree |
| 2012-04-03 |
Sarah Westcott | working on adding subsampling to dist.shared. fixed...
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commit | commitdiff | tree |
| 2012-04-02 |
Sarah Westcott | added create.database command. fixed help in get.sharedseqs...
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commit | commitdiff | tree |
| 2012-03-28 |
Sarah Westcott | mods to pcr.seqs
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commit | commitdiff | tree |
| 2012-03-28 |
Sarah Westcott | added keep dots to pcr.seqs. fixed pre.cluster name...
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commit | commitdiff | tree |
| 2012-03-28 |
Sarah Westcott | minor changes to pcr.seqs. Added filterToPos and filterFrom...
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commit | commitdiff | tree |
| 2012-03-27 |
Sarah Westcott | initialized numLinkers and numSpacers in trim.seqs...
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commit | commitdiff | tree |
| 2012-03-27 |
Sarah Westcott | added pcr.seqs command. fixed bug in rarefacftion.single...
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commit | commitdiff | tree |
| 2012-03-13 |
Sarah Westcott | fixed makefile
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commit | commitdiff | tree |
| 2012-03-13 |
Sarah Westcott | bug fix in linear algebra that caused an infinite loop
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commit | commitdiff | tree |
| 2012-03-13 |
Sarah Westcott | added unix to ifdefs. minor changes while testing 1...
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commit | commitdiff | tree |
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