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git.donarmstrong.com Git - mothur.git/log
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
westcott [Fri, 10 Dec 2010 14:50:00 +0000 (14:50 +0000)]
rolled back metastats workspace change
westcott [Fri, 10 Dec 2010 12:58:53 +0000 (12:58 +0000)]
added shared file to catchall command
westcott [Wed, 8 Dec 2010 21:51:24 +0000 (21:51 +0000)]
metastats double* to double fix for windows
westcott [Wed, 8 Dec 2010 17:39:56 +0000 (17:39 +0000)]
consensus.seqs summary file change
westcott [Wed, 8 Dec 2010 16:52:46 +0000 (16:52 +0000)]
get.oturep ifstream
westcott [Wed, 8 Dec 2010 16:37:28 +0000 (16:37 +0000)]
get.oturep change and trim.seqs fix
westcott [Wed, 8 Dec 2010 15:51:45 +0000 (15:51 +0000)]
catchall windows fix
westcott [Tue, 7 Dec 2010 17:14:58 +0000 (17:14 +0000)]
consensus.seqs can now find a consensus on a whole fasta file without needing a listfile
pschloss [Tue, 7 Dec 2010 13:14:09 +0000 (13:14 +0000)]
changes to seqerrorcommand
westcott [Tue, 7 Dec 2010 13:03:17 +0000 (13:03 +0000)]
fixed indicator grouping problem
westcott [Mon, 6 Dec 2010 22:35:06 +0000 (22:35 +0000)]
modified trim.seqs to speed up the append with multiple processors
westcott [Mon, 6 Dec 2010 12:47:44 +0000 (12:47 +0000)]
added summary output to catchall command
westcott [Fri, 3 Dec 2010 19:53:27 +0000 (19:53 +0000)]
fixed indicator command bug
westcott [Fri, 3 Dec 2010 11:08:08 +0000 (11:08 +0000)]
fixed craig nelsons weighted bug and paralellized parsimony
westcott [Mon, 29 Nov 2010 14:21:39 +0000 (14:21 +0000)]
added consensus.seqs command
westcott [Mon, 22 Nov 2010 19:43:24 +0000 (19:43 +0000)]
finished wrapper for catchall
westcott [Mon, 22 Nov 2010 13:24:01 +0000 (13:24 +0000)]
added group option to trim.seqs so you can provide your own groupfile instead of using an oligos file to make one.
westcott [Fri, 19 Nov 2010 13:12:27 +0000 (13:12 +0000)]
added indicator command
westcott [Fri, 12 Nov 2010 12:43:09 +0000 (12:43 +0000)]
added get.otus and remove.otus commands
westcott [Wed, 10 Nov 2010 14:39:31 +0000 (14:39 +0000)]
added get.groups and remove.groups commands
westcott [Wed, 10 Nov 2010 11:37:18 +0000 (11:37 +0000)]
finished sub.sample command
westcott [Tue, 9 Nov 2010 17:40:05 +0000 (17:40 +0000)]
parsimony calculator changed order of groups to reflect change in shared Utils made to make output of summary.shared match unifrac commands
westcott [Mon, 8 Nov 2010 14:40:33 +0000 (14:40 +0000)]
changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes
westcott [Mon, 8 Nov 2010 13:55:38 +0000 (13:55 +0000)]
fixed cluster.split bug
westcott [Mon, 8 Nov 2010 11:58:26 +0000 (11:58 +0000)]
cluster.split fix
westcott [Fri, 5 Nov 2010 20:02:24 +0000 (20:02 +0000)]
fixed metastats, added resize to cluster.classic, added code to kill children if parent is unable to spawn and dies.
westcott [Fri, 5 Nov 2010 19:26:09 +0000 (19:26 +0000)]
cluster.split fix
westcott [Tue, 2 Nov 2010 16:30:16 +0000 (16:30 +0000)]
changed cluster.classic so that it does not adjust the cutoff
westcott [Tue, 2 Nov 2010 15:14:07 +0000 (15:14 +0000)]
fixed bug with normalize.shared, printed out numbins twice. fixed bug with summary.single caused if you had too many groups to open all files at once.
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