Sarah Westcott [Tue, 11 Sep 2012 19:02:46 +0000 (15:02 -0400)]
added count file to get.groups and remove.groups. added shortcut parameter to classify.seqs.
Sarah Westcott [Fri, 7 Sep 2012 18:30:06 +0000 (14:30 -0400)]
major change to the tree class to use the count table class instead of tree map. This change involved changes to subsample class for trees, changes to the tree reader and readTree class. This change fixed bug with parsimony random tree generation that was leaving out the name file info. added count file to unifrac.unweighted, unifrac.weighted, parsimony, bin.seqs, classify.otu, classify.seqs, classify.tree, cluster.fragments, consensus.seqs, unique.seqs, phylo.diversity, summary.tax.
Sarah Westcott [Fri, 24 Aug 2012 14:55:14 +0000 (10:55 -0400)]
added sff.multiple command. fixed issue with windows paralellization in chimera.uchime with count file.
Sarah Westcott [Tue, 21 Aug 2012 17:39:22 +0000 (13:39 -0400)]
added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow for spitting the sff file by barcode. working on sff.multiple command.
Sarah Westcott [Tue, 14 Aug 2012 18:33:21 +0000 (14:33 -0400)]
added code to format fast files for uchime. started work on sff.multiple command
Sarah Westcott [Mon, 13 Aug 2012 19:17:19 +0000 (15:17 -0400)]
added count file to chimera.uchime. found issue with uchime program that indicated order mattered. added sort to mothur.h and reported to edgar.
Sarah Westcott [Wed, 8 Aug 2012 16:54:15 +0000 (12:54 -0400)]
added count parameter to chimera.slayer command
Sarah Westcott [Wed, 8 Aug 2012 15:07:46 +0000 (11:07 -0400)]
added SequenceCountParser class to parse the count table by group. added count parameter to chimera.perseus.
Sarah Westcott [Mon, 6 Aug 2012 12:38:00 +0000 (08:38 -0400)]
changes while testing 1.27
Sarah Westcott [Wed, 1 Aug 2012 15:08:39 +0000 (11:08 -0400)]
paralellized chop.seqs
Sarah Westcott [Tue, 31 Jul 2012 18:41:10 +0000 (14:41 -0400)]
added count file to cluster.classic and cluster.split. modified splitting classes to use the count file.
Sarah Westcott [Mon, 30 Jul 2012 19:25:39 +0000 (15:25 -0400)]
fixed subsample name file name issue. added count parameter to cluster command. added read to readColumn and readMatrix that uses a count table. added functions to countTable class to work with clusters reads.
Sarah Westcott [Fri, 27 Jul 2012 13:42:37 +0000 (09:42 -0400)]
added sparseDistanceMatrix class. Modified cluster commands to use the new sparse distance matrix class. cut cluster time by 55% and reduced memory usage by 50%.
Sarah Westcott [Wed, 11 Jul 2012 19:29:28 +0000 (15:29 -0400)]
working on adding count file to mgcluster
Sarah Westcott [Wed, 11 Jul 2012 19:09:35 +0000 (15:09 -0400)]
working on mgcluster count file change
Sarah Westcott [Wed, 11 Jul 2012 18:38:19 +0000 (14:38 -0400)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Wed, 11 Jul 2012 18:37:24 +0000 (14:37 -0400)]
added debug statements to trim.seqs
Kathryn Iverson [Wed, 11 Jul 2012 15:10:56 +0000 (11:10 -0400)]
merged mgcluster. kw files added, but not working in this commit!
Sarah Westcott [Tue, 10 Jul 2012 15:17:33 +0000 (11:17 -0400)]
changes while testing 1.26
Kathryn Iverson [Tue, 3 Jul 2012 19:01:16 +0000 (15:01 -0400)]
fixed pointers in mgcluster
Kathryn Iverson [Tue, 3 Jul 2012 18:53:29 +0000 (14:53 -0400)]
fixed kw parameter types
Kathryn Iverson [Tue, 3 Jul 2012 18:48:49 +0000 (14:48 -0400)]
updated mgcluster to take count file
Kathryn Iverson [Tue, 3 Jul 2012 16:47:57 +0000 (12:47 -0400)]
updated parameters for kw
Kathryn Iverson [Tue, 3 Jul 2012 16:40:45 +0000 (12:40 -0400)]
Merge branch 'master' of https://github.com/mothur/mothur.git into development
Sarah Westcott [Tue, 3 Jul 2012 15:40:16 +0000 (11:40 -0400)]
changes while testing 1.26
Kathryn Iverson [Mon, 2 Jul 2012 18:11:04 +0000 (14:11 -0400)]
updated getgroupnames
kdiverson [Mon, 2 Jul 2012 14:12:41 +0000 (10:12 -0400)]
fixed io
kdiverson [Mon, 2 Jul 2012 13:46:29 +0000 (09:46 -0400)]
cleaned up code2
kdiverson [Fri, 29 Jun 2012 20:07:26 +0000 (16:07 -0400)]
cleaned up code
kiverson [Fri, 29 Jun 2012 18:33:55 +0000 (14:33 -0400)]
removed comments
Kathryn Iverson [Thu, 28 Jun 2012 20:17:15 +0000 (16:17 -0400)]
updated kruskalwallis struct
Kathryn Iverson [Thu, 28 Jun 2012 15:59:02 +0000 (11:59 -0400)]
updated kruskalwallis struct
Sarah Westcott [Thu, 28 Jun 2012 13:37:34 +0000 (09:37 -0400)]
added countable class to read and store count file. added count parameter to make.shared command and modified sharedlistvector to use it. fixed formatting issue related to make.shared with a biom file.
Kathryn Iverson [Thu, 28 Jun 2012 13:31:03 +0000 (09:31 -0400)]
updated kruskalwallis command
Kathryn Iverson [Tue, 26 Jun 2012 19:43:31 +0000 (15:43 -0400)]
added kruskalwallis command
Sarah Westcott [Tue, 26 Jun 2012 15:27:14 +0000 (11:27 -0400)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Tue, 26 Jun 2012 15:25:18 +0000 (11:25 -0400)]
made make.table alias to count.seqs command. added large parameter to count.seqs to allow for creating the table without storing files in ram. added subsampling to rarefaction.shared. added countable current type.
Kathryn Iverson [Tue, 26 Jun 2012 15:03:11 +0000 (11:03 -0400)]
removed print statements from testing
Kathryn Iverson [Fri, 22 Jun 2012 21:10:10 +0000 (17:10 -0400)]
added large parameter to mgcluster along with new rabund support
kiverson [Fri, 22 Jun 2012 19:12:47 +0000 (15:12 -0400)]
removed comments
Kathryn Iverson [Thu, 21 Jun 2012 17:19:05 +0000 (13:19 -0400)]
edited createRabund function
Kathryn Iverson [Wed, 20 Jun 2012 21:34:14 +0000 (17:34 -0400)]
edited createRabund function
Kathryn Iverson [Wed, 20 Jun 2012 20:56:35 +0000 (16:56 -0400)]
added createRabund function to mgcluster
Kathryn Iverson [Wed, 20 Jun 2012 20:27:31 +0000 (16:27 -0400)]
added ifelse for rabund
Kathryn Iverson [Wed, 20 Jun 2012 20:22:52 +0000 (16:22 -0400)]
testing new devel branch
Sarah Westcott [Tue, 19 Jun 2012 18:09:38 +0000 (14:09 -0400)]
added phylip as output file type for commands that output distance matrices. added shared parameter to create.database command.
Sarah Westcott [Tue, 19 Jun 2012 12:48:32 +0000 (08:48 -0400)]
added load.logfile command. changed summary.single output for subsample=t.
Sarah Westcott [Tue, 12 Jun 2012 15:27:51 +0000 (11:27 -0400)]
changed reading of name file to use buffered reads. note the splitAtWhiteSpace function is sensitive to the gobble function. do not use the two together while reading or the read can get off track. modified trim.seqs group counts to include the redundant sees if a names file is provided. changed group maps read of a group file to be buffered. modified appendFiles functions to be buffered.
Sarah Westcott [Mon, 11 Jun 2012 16:13:55 +0000 (12:13 -0400)]
fixed bug with dist.shared subsampling. added mode parameter to dist.shared so you can select average or median for the results. added some debug code as I sorted out some bug reports to mothur.bugs.
Sarah Westcott [Tue, 5 Jun 2012 17:08:53 +0000 (13:08 -0400)]
added forward and reverse barcodes to trim.seqs to process illumina seqs
Sarah Westcott [Mon, 4 Jun 2012 19:40:50 +0000 (15:40 -0400)]
fixed classify.seqs output file name - had issue if reference taxonomy file did not have 3 parts to the name. modified rarefaction.shared to output a group.rarefaction file when design file is used.
Sarah Westcott [Mon, 4 Jun 2012 16:27:23 +0000 (12:27 -0400)]
added check to make sure shhh.flows child processes finish properly. added subsampling to summary.shared and summary.single. modified dist.shared to run original dataset as well as subsamples when subsample=t
Sarah Westcott [Tue, 29 May 2012 16:48:28 +0000 (12:48 -0400)]
added code to check path for uchime and catchall executables
Sarah Westcott [Thu, 24 May 2012 19:09:12 +0000 (15:09 -0400)]
forced rarefaction.single to output ending line for all groups. added subsample and iters parameters to summary.shared command.
Sarah Westcott [Thu, 24 May 2012 16:50:47 +0000 (12:50 -0400)]
fixed bug in sffinfo when ~ was used in the sff filename. fixed issue in shhh.flows, it was producing an output file called *.flow.fasta instead of *.fasta. Also when using outputdir with the file option, it put the shhh.fasta and shhh.names files in the wrong folder. changed format of rarefaction.single output with groups to look more like the phylo.diversity command.
Sarah Westcott [Wed, 23 May 2012 19:58:07 +0000 (15:58 -0400)]
added metadata parameter to otu.association
Sarah Westcott [Wed, 23 May 2012 18:33:47 +0000 (14:33 -0400)]
added design and sets parameters to the rarefaction.shared command. finished work on large parameter in shhh.flows.
Sarah Westcott [Tue, 22 May 2012 20:12:50 +0000 (16:12 -0400)]
added debug output classify.seqs. worked on make.contigs command. added large parameter to shhh.flows that divides the flow file.
Sarah Westcott [Mon, 21 May 2012 18:00:07 +0000 (14:00 -0400)]
added get.otulabels and remove.otulabels commands per user request
Sarah Westcott [Fri, 18 May 2012 19:16:09 +0000 (15:16 -0400)]
added threshold parameter to make.contigs command.
Sarah Westcott [Fri, 18 May 2012 16:38:00 +0000 (12:38 -0400)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Fri, 18 May 2012 16:35:51 +0000 (12:35 -0400)]
added check to cluster.classic to make sure file type is phylip. added mapping function to alignments traceback function so we can relate the position in the unaligned sequence to the aligned sequence. worked on make.contigs command
Kathryn Iverson [Wed, 16 May 2012 20:30:08 +0000 (16:30 -0400)]
added check for numOTUS, will skip if < 2.
Kathryn Iverson [Wed, 16 May 2012 17:59:17 +0000 (13:59 -0400)]
Merge branch 'master' of https://github.com/mothur/mothur.git
Kathryn Iverson [Wed, 16 May 2012 17:54:52 +0000 (13:54 -0400)]
updated output to include standard deviation
Kathryn Iverson [Wed, 16 May 2012 17:52:24 +0000 (13:52 -0400)]
replaced p-value with zscore for lookup in ztable.
Sarah Westcott [Wed, 16 May 2012 14:04:50 +0000 (10:04 -0400)]
added classic parameter to cluster.split. working on make.contigs command. fixed bug in align.seqs with align=blast - caused segfault.
Kathryn Iverson [Tue, 15 May 2012 20:29:33 +0000 (16:29 -0400)]
added functions to calculate standard deviation and zscore
Sarah Westcott [Tue, 15 May 2012 17:54:41 +0000 (13:54 -0400)]
added list.labels command. started work on make.contigs command. fixed fastq.info and make.fastq quality scores control character. fixed bug in classify.otu that made bootstrap values for "unknown" taxon too high
Sarah Westcott [Mon, 14 May 2012 17:49:25 +0000 (13:49 -0400)]
last checkin for 1.25.1
Sarah Westcott [Mon, 14 May 2012 16:20:43 +0000 (12:20 -0400)]
fixed bug in make.biom that occurred if some taxonomies had confidence scores and others did not.
Sarah Westcott [Mon, 14 May 2012 13:30:26 +0000 (09:30 -0400)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Mon, 14 May 2012 13:29:16 +0000 (09:29 -0400)]
added debug info to engines function to get mother's path
John Westcott [Mon, 14 May 2012 13:28:01 +0000 (09:28 -0400)]
trying to clean up project files path issues
Pat Schloss [Mon, 14 May 2012 12:39:11 +0000 (08:39 -0400)]
fixing pbxproj
Pat Schloss [Mon, 14 May 2012 12:07:32 +0000 (08:07 -0400)]
Merge remote-tracking branch 'mothur/master'
Pat Schloss [Mon, 14 May 2012 12:06:50 +0000 (08:06 -0400)]
small mods to sensspec command
Sarah Westcott [Fri, 11 May 2012 17:47:32 +0000 (13:47 -0400)]
added some debug stuff to chimera.uchime. optimized phylo.diversity to improve rarefy speed.
Sarah Westcott [Fri, 11 May 2012 11:22:19 +0000 (07:22 -0400)]
fixed path redirect issue in shhh.flows. optimized the subsampling in unifrac commands
Sarah Westcott [Thu, 10 May 2012 17:17:57 +0000 (13:17 -0400)]
fixed typos
Sarah Westcott [Thu, 10 May 2012 14:11:38 +0000 (10:11 -0400)]
added abundance and sample parameters to get.coremicrobiome command.
Sarah Westcott [Wed, 9 May 2012 16:47:34 +0000 (12:47 -0400)]
working on get.coremicrobiom
John Westcott [Wed, 9 May 2012 15:34:37 +0000 (11:34 -0400)]
Merge remote-tracking branch 'origin/master'
John Westcott [Wed, 9 May 2012 15:31:46 +0000 (11:31 -0400)]
added debug flag to mothurOut. added debug parameter to set.dir. added debug code to catchall and get.seqs commands. created newcommandtemplate. started work on get.coremicrobiom command. fixed command parameter bug in chimera.bellerophon command.
Sarah Westcott [Wed, 9 May 2012 13:02:37 +0000 (09:02 -0400)]
cluster.split split method defaults to classify if taxonomy file is given with no fast file.
Sarah Westcott [Wed, 2 May 2012 19:22:40 +0000 (15:22 -0400)]
fixed segfault in unifrac with subsample. in progress of implementing a version of the subsample tree that sets sees you don't want to includes groups to doNotIncludeMe. to test which is more efficient.
Sarah Westcott [Wed, 2 May 2012 16:03:00 +0000 (12:03 -0400)]
Revert to previous commit
Sarah Westcott [Wed, 2 May 2012 15:53:52 +0000 (11:53 -0400)]
fixing
Sarah Westcott [Wed, 2 May 2012 15:39:37 +0000 (11:39 -0400)]
moving source to source folder
Sarah Westcott [Wed, 2 May 2012 15:38:02 +0000 (11:38 -0400)]
moved mothur's source into a folder to make grabbing just the source easier on github
Sarah Westcott [Wed, 2 May 2012 15:19:21 +0000 (11:19 -0400)]
removing chime source files from mother project.
Sarah Westcott [Wed, 2 May 2012 12:05:07 +0000 (08:05 -0400)]
another test
Sarah Westcott [Wed, 2 May 2012 12:03:21 +0000 (08:03 -0400)]
test2
Sarah Westcott [Wed, 2 May 2012 11:17:34 +0000 (07:17 -0400)]
test commit
John Westcott [Tue, 1 May 2012 18:49:02 +0000 (14:49 -0400)]
commit test
Pat Schloss [Tue, 1 May 2012 18:01:13 +0000 (14:01 -0400)]
Merge remote-tracking branch 'mothur/master'
Pat Schloss [Tue, 1 May 2012 18:00:53 +0000 (14:00 -0400)]
fix rarefaction.single
Sarah Westcott [Tue, 1 May 2012 15:18:19 +0000 (11:18 -0400)]
Merge remote-tracking branch 'mothur/master'
Sarah Westcott [Tue, 1 May 2012 15:17:36 +0000 (11:17 -0400)]
bug in dist.shared and tree.shared with new subsampling code when groups were eliminated the numgroups and lines were not updated.
Kathryn Iverson [Tue, 1 May 2012 15:10:31 +0000 (11:10 -0400)]
fixed sim9 and trial_swap