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git.donarmstrong.com Git - mothur.git/log
westcott [Fri, 4 Mar 2011 13:22:24 +0000 (13:22 +0000)]
bug fixes
pschloss [Thu, 3 Mar 2011 22:57:03 +0000 (22:57 +0000)]
fixed bug in seqerrorcommand
pschloss [Thu, 3 Mar 2011 22:43:48 +0000 (22:43 +0000)]
took out couts
pschloss [Thu, 3 Mar 2011 22:41:20 +0000 (22:41 +0000)]
modified reportfile class
pschloss [Thu, 3 Mar 2011 21:40:53 +0000 (21:40 +0000)]
modified seqerror and qualscores
pschloss [Thu, 3 Mar 2011 21:40:52 +0000 (21:40 +0000)]
modified seqerror and qualscores
westcott [Mon, 28 Feb 2011 12:08:07 +0000 (12:08 +0000)]
fixed unweighted command
pschloss [Sat, 26 Feb 2011 20:12:42 +0000 (20:12 +0000)]
some minor changes
westcott [Fri, 25 Feb 2011 11:22:02 +0000 (11:22 +0000)]
changed version and release date
westcott [Fri, 25 Feb 2011 11:13:46 +0000 (11:13 +0000)]
added root parameter to the unifrac commands so you can choose to include the entire root or stop the calc at the "root" of the comparison.
westcott [Wed, 23 Feb 2011 21:56:08 +0000 (21:56 +0000)]
fixed bug in unifrac commands with nexus translation if files don't match
westcott [Wed, 23 Feb 2011 21:56:08 +0000 (21:56 +0000)]
fixed bug in unifrac commands with nexus translation if files don't match
westcott [Wed, 23 Feb 2011 18:34:53 +0000 (18:34 +0000)]
fixed bug in unifrac commands with unrooted trees
westcott [Wed, 23 Feb 2011 13:34:08 +0000 (13:34 +0000)]
fixed bug in unifrac commands with unrooted trees
pschloss [Mon, 21 Feb 2011 21:14:58 +0000 (21:14 +0000)]
reworked amova / homova / anosim
westcott [Fri, 18 Feb 2011 15:14:03 +0000 (15:14 +0000)]
fixed unifrac bug with multiple processors if numComps was less than processors. fixed bug with random number generator for sub.sample command.
pschloss [Fri, 18 Feb 2011 14:27:42 +0000 (14:27 +0000)]
mods to amova command
pschloss [Wed, 16 Feb 2011 11:47:54 +0000 (11:47 +0000)]
bug fix to seq.error
westcott [Tue, 15 Feb 2011 20:38:42 +0000 (20:38 +0000)]
finished anosim command
pschloss [Tue, 15 Feb 2011 19:48:17 +0000 (19:48 +0000)]
fixed an mpi bug in shhh.seqs
westcott [Tue, 15 Feb 2011 19:00:01 +0000 (19:00 +0000)]
working on anosim command
pschloss [Tue, 15 Feb 2011 18:33:02 +0000 (18:33 +0000)]
took cout's from shhh.seqs
pschloss [Tue, 15 Feb 2011 18:29:26 +0000 (18:29 +0000)]
fixed bugg in shhh.seqs command
westcott [Tue, 15 Feb 2011 17:47:03 +0000 (17:47 +0000)]
finished the chimera.slayer split function
westcott [Tue, 15 Feb 2011 12:11:22 +0000 (12:11 +0000)]
fixed mpi version compile issue with chimera.slayer
pschloss [Tue, 15 Feb 2011 11:41:28 +0000 (11:41 +0000)]
mods to shhh.seqs command
pschloss [Tue, 15 Feb 2011 11:17:04 +0000 (11:17 +0000)]
mods to seq.errror
westcott [Mon, 14 Feb 2011 18:54:13 +0000 (18:54 +0000)]
added make.fastq command
westcott [Mon, 14 Feb 2011 15:13:23 +0000 (15:13 +0000)]
fixed catchall PATH variable bug added trimera to chimera.slayer
pschloss [Mon, 14 Feb 2011 12:07:53 +0000 (12:07 +0000)]
*** empty log message ***
pschloss [Fri, 11 Feb 2011 22:10:56 +0000 (22:10 +0000)]
mod to seq.error to allow for degenerate bases in the ref sequences
pschloss [Fri, 11 Feb 2011 12:32:21 +0000 (12:32 +0000)]
shhh.seqs and trim.flows modifications.
pschloss [Thu, 10 Feb 2011 18:53:01 +0000 (18:53 +0000)]
modified reverse.seqs and qualscores.cpp
pschloss [Wed, 9 Feb 2011 20:22:07 +0000 (20:22 +0000)]
mods to trim.seqs
pschloss [Wed, 9 Feb 2011 20:22:07 +0000 (20:22 +0000)]
mods to trim.seqs
westcott [Wed, 9 Feb 2011 18:17:22 +0000 (18:17 +0000)]
added mantel command
westcott [Wed, 9 Feb 2011 17:18:48 +0000 (17:18 +0000)]
added mantel command
pschloss [Wed, 9 Feb 2011 15:25:04 +0000 (15:25 +0000)]
mods to shhhercommand and seqerrorcommand
pschloss [Tue, 8 Feb 2011 21:49:42 +0000 (21:49 +0000)]
changes to trim.flows command
westcott [Tue, 8 Feb 2011 17:56:37 +0000 (17:56 +0000)]
added [ERROR] flag if command aborts
westcott [Tue, 8 Feb 2011 16:24:38 +0000 (16:24 +0000)]
fixed homova command
westcott [Tue, 8 Feb 2011 16:07:55 +0000 (16:07 +0000)]
added homova command
westcott [Tue, 8 Feb 2011 15:42:06 +0000 (15:42 +0000)]
added homova command
westcott [Tue, 8 Feb 2011 12:41:30 +0000 (12:41 +0000)]
added amova command
westcott [Tue, 8 Feb 2011 12:29:23 +0000 (12:29 +0000)]
added amova command
westcott [Tue, 8 Feb 2011 12:03:48 +0000 (12:03 +0000)]
added amova command
westcott [Mon, 7 Feb 2011 14:15:06 +0000 (14:15 +0000)]
adding license
westcott [Fri, 4 Feb 2011 20:49:06 +0000 (20:49 +0000)]
fixed kendall method in corr.axes
westcott [Fri, 4 Feb 2011 15:31:12 +0000 (15:31 +0000)]
working on kendall
pschloss [Fri, 4 Feb 2011 14:32:50 +0000 (14:32 +0000)]
removed trimera checking from refchimeratest
westcott [Fri, 4 Feb 2011 12:54:38 +0000 (12:54 +0000)]
fixed catchall hangup if it can't find the exe
westcott [Thu, 3 Feb 2011 20:44:08 +0000 (20:44 +0000)]
corr.axes spearman
westcott [Thu, 3 Feb 2011 16:44:19 +0000 (16:44 +0000)]
changes for 1.16.0
pschloss [Thu, 3 Feb 2011 12:29:43 +0000 (12:29 +0000)]
true chimera testing using reference sequences
pschloss [Thu, 3 Feb 2011 12:29:09 +0000 (12:29 +0000)]
*** empty log message ***
westcott [Wed, 26 Jan 2011 18:45:51 +0000 (18:45 +0000)]
fixed mempearson and structpearson
westcott [Wed, 26 Jan 2011 17:57:33 +0000 (17:57 +0000)]
mods in testing 1.16.0
westcott [Tue, 25 Jan 2011 18:50:16 +0000 (18:50 +0000)]
mods for 1.16
westcott [Mon, 24 Jan 2011 18:50:52 +0000 (18:50 +0000)]
added merge.groups command
westcott [Mon, 24 Jan 2011 18:03:06 +0000 (18:03 +0000)]
added zscore method to normalize.shared
westcott [Mon, 24 Jan 2011 14:16:21 +0000 (14:16 +0000)]
remove.rare command
westcott [Fri, 21 Jan 2011 19:22:04 +0000 (19:22 +0000)]
modified shhhercommand to make buildable with windows
westcott [Fri, 21 Jan 2011 19:16:14 +0000 (19:16 +0000)]
added calcs to tree.shared. working on remove.rare command
westcott [Fri, 21 Jan 2011 15:29:36 +0000 (15:29 +0000)]
added diffs and percent parameters to cluster.fragments command
westcott [Fri, 21 Jan 2011 13:35:24 +0000 (13:35 +0000)]
nmds command done
westcott [Fri, 21 Jan 2011 13:29:37 +0000 (13:29 +0000)]
working on nmds
westcott [Fri, 21 Jan 2011 12:54:26 +0000 (12:54 +0000)]
working on nmds
westcott [Wed, 19 Jan 2011 18:41:56 +0000 (18:41 +0000)]
working on nmds command
westcott [Wed, 19 Jan 2011 18:31:21 +0000 (18:31 +0000)]
working on nmds command
westcott [Fri, 14 Jan 2011 16:09:49 +0000 (16:09 +0000)]
fixed trim.seqs bug with qtrim parameter and added num=1 special case to database search classes
westcott [Mon, 10 Jan 2011 18:12:21 +0000 (18:12 +0000)]
pca command
westcott [Mon, 10 Jan 2011 17:39:51 +0000 (17:39 +0000)]
pca command
westcott [Fri, 7 Jan 2011 18:18:59 +0000 (18:18 +0000)]
finished chimera.slayer adding trim parameter, added persample parameter to sub.sample command and create linearalgebra class
westcott [Fri, 7 Jan 2011 15:37:56 +0000 (15:37 +0000)]
working on chimera change to add trim feature, fixed bug in print of distance file for unifrac.weighted and unifrac.unweighted that caused distances to be in the wrong order.
westcott [Wed, 5 Jan 2011 16:23:50 +0000 (16:23 +0000)]
added pearson coefficient metric to pcoa
westcott [Wed, 5 Jan 2011 13:42:03 +0000 (13:42 +0000)]
changed filename of pcacommand to pcoacommand
westcott [Wed, 5 Jan 2011 13:07:39 +0000 (13:07 +0000)]
removed various build warnings
westcott [Wed, 5 Jan 2011 11:37:25 +0000 (11:37 +0000)]
added metadata file as input to corr.axes
westcott [Tue, 4 Jan 2011 18:41:51 +0000 (18:41 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 18:41:42 +0000 (18:41 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 18:35:45 +0000 (18:35 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 15:40:55 +0000 (15:40 +0000)]
removed parse.sff command and made its functionality part of sffinfo command. fixed issues with corr.axes method=kendall.
pschloss [Tue, 4 Jan 2011 11:54:21 +0000 (11:54 +0000)]
modifications to shhh.seqs
westcott [Mon, 3 Jan 2011 19:16:52 +0000 (19:16 +0000)]
added template=self capability to chimers.slayer, worked on corr.axes and added accnos compare function to get.seqs
pschloss [Fri, 31 Dec 2010 16:42:32 +0000 (16:42 +0000)]
added shhh.seqs command
pschloss [Fri, 31 Dec 2010 16:35:11 +0000 (16:35 +0000)]
added shhh.seqs command
pschloss [Thu, 23 Dec 2010 21:37:11 +0000 (21:37 +0000)]
addition of trim.flows
westcott [Thu, 23 Dec 2010 19:41:30 +0000 (19:41 +0000)]
fixed memory leak in maligner minCoverageFilter function used by chimera slayer
westcott [Thu, 23 Dec 2010 19:05:17 +0000 (19:05 +0000)]
fixed memory leak in decalc findClosest function used by chimera slayer
westcott [Wed, 22 Dec 2010 19:03:19 +0000 (19:03 +0000)]
chimera.slayer fix
westcott [Wed, 22 Dec 2010 14:58:11 +0000 (14:58 +0000)]
fixed trim.seqs weird characters thing
westcott [Wed, 22 Dec 2010 13:22:04 +0000 (13:22 +0000)]
added output filenames and m->control_pressed stuff to seq.error command
pschloss [Tue, 21 Dec 2010 20:35:44 +0000 (20:35 +0000)]
more changes to error.seqs command and quality scores classses
pschloss [Mon, 20 Dec 2010 12:29:36 +0000 (12:29 +0000)]
pat's changes to seq.error command
westcott [Fri, 17 Dec 2010 18:54:42 +0000 (18:54 +0000)]
added design parameter to the indicator command
westcott [Fri, 17 Dec 2010 16:46:03 +0000 (16:46 +0000)]
added odum, canberra, structchi2, structchord, structeuclidean, gower, hellinger, structkulczynski, manhattan, structpearson, soergel, spearman, speciesprofile, memchi2, memchord, memeuclidean, hamming, mempearson calcs
westcott [Fri, 17 Dec 2010 13:47:10 +0000 (13:47 +0000)]
fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it, but since multiple barcodes went to the same group the allfiles list had the same name more than once, so when it went to check if it was blank again it didn't exist
westcott [Tue, 14 Dec 2010 14:03:00 +0000 (14:03 +0000)]
added confidence scores to get.lineage and remove.lineage
westcott [Mon, 13 Dec 2010 20:33:34 +0000 (20:33 +0000)]
added summary file to classify.otu
westcott [Mon, 13 Dec 2010 13:55:30 +0000 (13:55 +0000)]
classify.seqs summary file fix
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