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git.donarmstrong.com Git - mothur.git/log
westcott [Wed, 5 May 2010 14:10:34 +0000 (14:10 +0000)]
filled out reference taxonomy with "unclassified" so that if a cutoff is used the summary file still adds up
westcott [Tue, 4 May 2010 15:05:05 +0000 (15:05 +0000)]
enabled ~
westcott [Tue, 4 May 2010 13:45:52 +0000 (13:45 +0000)]
fixed bug that caused bayesian cutoff not to work if iters > 100. fixed bug in trim.seqs caused by sequence length for qfile coming from fasta file.
westcott [Tue, 4 May 2010 12:41:07 +0000 (12:41 +0000)]
added phylo.diversity command. added hard parameter to cluster, hcluster and read.dist. modified remove.seqs so it can do multiple files at once.
westcott [Fri, 30 Apr 2010 13:50:47 +0000 (13:50 +0000)]
made get.oturep more memory efficient by breaking the work into 2 pieces.
westcott [Fri, 30 Apr 2010 12:01:35 +0000 (12:01 +0000)]
paralellized trim.seqs
westcott [Thu, 29 Apr 2010 13:54:23 +0000 (13:54 +0000)]
paralellized summary.seqs and added mpi code to it.
westcott [Thu, 29 Apr 2010 11:15:33 +0000 (11:15 +0000)]
paralellized screen.seqs and added mpi code to it. fixed bug with all mpi commands that was caused by the startindex line coming after the numSeqsPerProcess line, only occurred in files where the number of seqs could not be divide evenly between processes.
westcott [Wed, 28 Apr 2010 11:09:48 +0000 (11:09 +0000)]
added set.logfile command
westcott [Tue, 27 Apr 2010 18:53:09 +0000 (18:53 +0000)]
added name parameter to phylotype command
westcott [Tue, 27 Apr 2010 17:54:59 +0000 (17:54 +0000)]
reworked the classifiers summary file added groupfile option to classify.seqs, added mpi code to classifiers modification
westcott [Mon, 26 Apr 2010 15:05:21 +0000 (15:05 +0000)]
made classifier faster
westcott [Tue, 20 Apr 2010 12:50:01 +0000 (12:50 +0000)]
a few modifications for 1.9
westcott [Tue, 20 Apr 2010 11:34:53 +0000 (11:34 +0000)]
a few modifications for 1.9
westcott [Sat, 17 Apr 2010 00:10:32 +0000 (00:10 +0000)]
1.9
westcott [Fri, 16 Apr 2010 14:55:17 +0000 (14:55 +0000)]
1.9
pschloss [Wed, 14 Apr 2010 12:44:12 +0000 (12:44 +0000)]
pat's minor edits to distance calculations
westcott [Wed, 14 Apr 2010 11:32:59 +0000 (11:32 +0000)]
some changes while testing 1.9
westcott [Wed, 7 Apr 2010 12:55:09 +0000 (12:55 +0000)]
added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff, paralellized filter.seqs and bellerophon.
westcott [Wed, 17 Mar 2010 17:47:33 +0000 (17:47 +0000)]
finished mpi for filter.seqs
westcott [Wed, 17 Mar 2010 14:59:45 +0000 (14:59 +0000)]
testing
westcott [Tue, 16 Mar 2010 13:09:20 +0000 (13:09 +0000)]
modified mpi code to save ram by writing out every 10 seqs.
westcott [Fri, 12 Mar 2010 17:39:18 +0000 (17:39 +0000)]
added MPI to dist.seqs command
westcott [Thu, 11 Mar 2010 13:20:55 +0000 (13:20 +0000)]
testing mpi
westcott [Thu, 4 Mar 2010 18:35:56 +0000 (18:35 +0000)]
mothur with external build
westcott [Thu, 4 Mar 2010 14:50:33 +0000 (14:50 +0000)]
changes to filter.seqs
westcott [Wed, 3 Mar 2010 12:33:53 +0000 (12:33 +0000)]
added checks for ^C to quit command instead of program
westcott [Mon, 1 Mar 2010 11:59:21 +0000 (11:59 +0000)]
adding mothurout.h and .cpp to repo
westcott [Fri, 26 Feb 2010 15:08:15 +0000 (15:08 +0000)]
filter.seqs can now accept multiple fasta files
westcott [Fri, 26 Feb 2010 14:35:09 +0000 (14:35 +0000)]
created mothurOut class to handle logfiles
westcott [Thu, 25 Feb 2010 12:05:21 +0000 (12:05 +0000)]
added parse.list command
westcott [Wed, 24 Feb 2010 11:07:33 +0000 (11:07 +0000)]
finished chimera changes
westcott [Tue, 23 Feb 2010 19:41:26 +0000 (19:41 +0000)]
added warning about merging with something above cutoff to cluster. working on chimeras
westcott [Tue, 23 Feb 2010 19:31:30 +0000 (19:31 +0000)]
added warning about merging with something above cutoff to cluster. working on chimeras
westcott [Mon, 22 Feb 2010 17:22:22 +0000 (17:22 +0000)]
chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector to step out of bounds
westcott [Wed, 17 Feb 2010 13:30:52 +0000 (13:30 +0000)]
chimeras
westcott [Tue, 16 Feb 2010 15:23:05 +0000 (15:23 +0000)]
chimeracode
westcott [Fri, 12 Feb 2010 19:50:54 +0000 (19:50 +0000)]
working on chimeras
pschloss [Thu, 4 Feb 2010 21:06:01 +0000 (21:06 +0000)]
test
pschloss [Thu, 4 Feb 2010 15:57:46 +0000 (15:57 +0000)]
pat's ../ bug fix - test
pschloss [Thu, 4 Feb 2010 15:14:07 +0000 (15:14 +0000)]
pat's ../ bug fix
westcott [Wed, 3 Feb 2010 12:26:44 +0000 (12:26 +0000)]
added name option to read.tree for use in unifrac and parimony commands
pschloss [Tue, 2 Feb 2010 15:00:23 +0000 (15:00 +0000)]
pat's differences before v.1.8
westcott [Tue, 2 Feb 2010 14:33:49 +0000 (14:33 +0000)]
fixed bugs for 1.8
westcott [Thu, 28 Jan 2010 18:11:16 +0000 (18:11 +0000)]
fixed some bugs found while testing 1.8
westcott [Wed, 27 Jan 2010 21:08:49 +0000 (21:08 +0000)]
fixed some bugs found while testing 1.8
westcott [Wed, 27 Jan 2010 16:04:47 +0000 (16:04 +0000)]
added distance search method to classify.seqs
westcott [Tue, 26 Jan 2010 19:36:30 +0000 (19:36 +0000)]
added set.dir command and modified commands to redirect input and output, removed get.line command.
pschloss [Tue, 26 Jan 2010 18:13:06 +0000 (18:13 +0000)]
pat's edits from 1/26/2010
westcott [Tue, 19 Jan 2010 18:15:34 +0000 (18:15 +0000)]
added out.hierarchy command
pschloss [Tue, 19 Jan 2010 14:20:22 +0000 (14:20 +0000)]
pat's mods to morisitahorn and pre.cluster
westcott [Tue, 19 Jan 2010 13:48:32 +0000 (13:48 +0000)]
added warning about average neighbor merges around cutoff. fixed little bugs.
westcott [Thu, 14 Jan 2010 16:13:32 +0000 (16:13 +0000)]
added formatmatrix, formatcolumn, and formatphylip classes. Used these classes in get.oturep to make it able to process distance matrices too large to fit in RAM. added output of .rep.names file to get.oturep command
westcott [Tue, 12 Jan 2010 19:00:34 +0000 (19:00 +0000)]
worked on hcluster. made .single command run using a sharedfile. and various other small changes
westcott [Tue, 5 Jan 2010 21:29:35 +0000 (21:29 +0000)]
you can now use a distance matrix as input for the heatmap.sim command.
added distance parameter to unifrac.weighted and unifrac.unweighted commands that allows you to output a distance matrix from the command.
added random parameter to unifrac.weighted and unifrac.unweighted commands that allows you to shut off the comparison to random trees.
westcott [Mon, 4 Jan 2010 18:12:00 +0000 (18:12 +0000)]
added pca command
westcott [Wed, 23 Dec 2009 19:16:36 +0000 (19:16 +0000)]
added average and nearest neighbor methods to hcluster
westcott [Wed, 23 Dec 2009 18:47:52 +0000 (18:47 +0000)]
precluster command finished
westcott [Mon, 21 Dec 2009 15:03:14 +0000 (15:03 +0000)]
fixed some bugs and added mgcluster command
westcott [Wed, 9 Dec 2009 19:56:36 +0000 (19:56 +0000)]
added sorted parameter to get.oturep, added error checking to chimera classes in case unaligned sequences are used where aligned are expected and added probs parameter to classify.seqs to shut off bootstrapping with bayesian method
westcott [Tue, 8 Dec 2009 17:20:43 +0000 (17:20 +0000)]
added list parameter to get.seqs and remove.seqs and added readline library for interact engine
westcott [Wed, 2 Dec 2009 20:11:35 +0000 (20:11 +0000)]
modified sequence class to read fasta files with comments. this required modifications to several other files that use sequence. also added flip and threshold parameter to align.seqs command
westcott [Wed, 25 Nov 2009 16:50:42 +0000 (16:50 +0000)]
a few changes to chimera classes
pschloss [Wed, 25 Nov 2009 12:17:10 +0000 (12:17 +0000)]
version for 10.5
westcott [Tue, 24 Nov 2009 19:29:37 +0000 (19:29 +0000)]
changed get.sharedotu to get.sharedseqs
pschloss [Tue, 24 Nov 2009 16:29:42 +0000 (16:29 +0000)]
fixed splash page citation
westcott [Tue, 24 Nov 2009 14:10:08 +0000 (14:10 +0000)]
changed get.sharedotu to get.sharedseqs
westcott [Tue, 24 Nov 2009 12:41:40 +0000 (12:41 +0000)]
fixed bug in hcluster command
westcott [Mon, 23 Nov 2009 19:24:47 +0000 (19:24 +0000)]
edited taxonomy equalizer to fix bug with windows
westcott [Mon, 23 Nov 2009 18:57:03 +0000 (18:57 +0000)]
updated phylotype command
westcott [Mon, 23 Nov 2009 18:40:54 +0000 (18:40 +0000)]
changed label outputs for phylotype command
westcott [Mon, 23 Nov 2009 17:27:06 +0000 (17:27 +0000)]
added phylotype command which reads a taxonomy file and creates a .list, .rabund and .sabund file.
westcott [Thu, 19 Nov 2009 20:04:04 +0000 (20:04 +0000)]
fixed bug in libshuff
westcott [Tue, 17 Nov 2009 17:14:58 +0000 (17:14 +0000)]
final fixes for 1.7
westcott [Fri, 13 Nov 2009 16:01:14 +0000 (16:01 +0000)]
finished work on classify.seqs bayesian method and various bug fixes
westcott [Thu, 5 Nov 2009 14:40:15 +0000 (14:40 +0000)]
started work on classify.seqs command. changed the database class so that it does not store the template sequences. created alignmentDB class that stores template seqs and uses database class for searching. made changes to aligncommand and chimeracheckrdp to reflect the changes to database class.
westcott [Mon, 2 Nov 2009 15:43:43 +0000 (15:43 +0000)]
added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get.oturep that started bin numbers at 0, finished work on hcluster command.
westcott [Thu, 29 Oct 2009 18:17:36 +0000 (18:17 +0000)]
fixed bug with hcluster
westcott [Thu, 29 Oct 2009 13:56:37 +0000 (13:56 +0000)]
added hcluster command and fixed some bugs, namely one with smart distancing.
westcott [Mon, 12 Oct 2009 21:26:13 +0000 (21:26 +0000)]
finished chimeraslayer method and added get.listcount command
westcott [Tue, 29 Sep 2009 16:05:10 +0000 (16:05 +0000)]
working on chimeraslayer and found bug in shared command.
westcott [Mon, 28 Sep 2009 14:31:48 +0000 (14:31 +0000)]
started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstructor
westcott [Wed, 23 Sep 2009 13:32:40 +0000 (13:32 +0000)]
added get.sharedotu command
westcott [Tue, 22 Sep 2009 14:16:08 +0000 (14:16 +0000)]
removed line option
westcott [Mon, 21 Sep 2009 13:19:02 +0000 (13:19 +0000)]
align.check command added
westcott [Fri, 18 Sep 2009 17:38:21 +0000 (17:38 +0000)]
adding more error checking for list and group files. outputs missing.names or missing.group if you have files with different number of sequences in them
westcott [Fri, 18 Sep 2009 12:19:52 +0000 (12:19 +0000)]
removing extra file output from pintail
westcott [Thu, 17 Sep 2009 13:48:20 +0000 (13:48 +0000)]
added check for blank files in openInputFile, add check for groupfiles that contain more seqs than the list files in sharedcommand
westcott [Tue, 15 Sep 2009 17:43:32 +0000 (17:43 +0000)]
fixed some issues while testing 1.6
westcott [Mon, 14 Sep 2009 15:01:48 +0000 (15:01 +0000)]
added help to chimera.seqs
westcott [Fri, 11 Sep 2009 16:28:24 +0000 (16:28 +0000)]
chimeracheck method added
westcott [Wed, 9 Sep 2009 20:20:23 +0000 (20:20 +0000)]
continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due to the fact that we changed the sequence class so that all seqs now have an aligned version. that change was made to fix another bug.
westcott [Tue, 8 Sep 2009 13:53:16 +0000 (13:53 +0000)]
finished with ccode, returned bellerophon to last save before move, cleaned up pintails outputs
westcott [Fri, 4 Sep 2009 16:01:17 +0000 (16:01 +0000)]
changed reporting in ccode to only report those who are found to be chimeric by all three tests, also fixed issue with the masking
westcott [Fri, 4 Sep 2009 15:06:54 +0000 (15:06 +0000)]
ccode working - still need to paralellize
westcott [Wed, 2 Sep 2009 09:50:25 +0000 (09:50 +0000)]
updated pats contact and mothur header info
westcott [Tue, 1 Sep 2009 19:16:29 +0000 (19:16 +0000)]
changed raredisplay to use vectors instead of files
westcott [Tue, 1 Sep 2009 12:17:14 +0000 (12:17 +0000)]
added more descriptive error messages to sharedlist
westcott [Mon, 31 Aug 2009 14:33:57 +0000 (14:33 +0000)]
checking in chimera files in progress after move to michigan
westcott [Thu, 13 Aug 2009 14:36:07 +0000 (14:36 +0000)]
last changes before move