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git.donarmstrong.com Git - mothur.git/log
pschloss [Wed, 27 Apr 2011 10:22:58 +0000 (10:22 +0000)]
tracking down chimera.slayer issue
westcott [Tue, 26 Apr 2011 19:44:22 +0000 (19:44 +0000)]
added current as option is lists of file names, processors now outputted with current options added flow type to current files, added queryName != templateName in decalc.findclosest for slayer
westcott [Tue, 26 Apr 2011 11:45:58 +0000 (11:45 +0000)]
blast queryName=templateSeq name bug
westcott [Tue, 26 Apr 2011 11:40:11 +0000 (11:40 +0000)]
*** empty log message ***
westcott [Mon, 25 Apr 2011 18:00:39 +0000 (18:00 +0000)]
minor bug in chimera maligner
westcott [Mon, 25 Apr 2011 11:31:20 +0000 (11:31 +0000)]
fixed ties issue in maligner getBlastSeqs
pschloss [Thu, 21 Apr 2011 20:08:54 +0000 (20:08 +0000)]
small things with chimera.slayer
pschloss [Wed, 20 Apr 2011 16:54:49 +0000 (16:54 +0000)]
some alterations to chimera.slayer
westcott [Tue, 19 Apr 2011 10:08:17 +0000 (10:08 +0000)]
finished chimera.slayer template=self change
westcott [Mon, 18 Apr 2011 17:55:59 +0000 (17:55 +0000)]
modified chimera.slayer template=self
pschloss [Mon, 18 Apr 2011 17:25:11 +0000 (17:25 +0000)]
small fix to refchimeratest.cpp
pschloss [Mon, 18 Apr 2011 15:01:44 +0000 (15:01 +0000)]
tie breaker fix to chimera.slayer
pschloss [Mon, 18 Apr 2011 14:08:31 +0000 (14:08 +0000)]
tie breaker fix to chimera.slayer
westcott [Fri, 15 Apr 2011 15:25:08 +0000 (15:25 +0000)]
1.18.1
westcott [Mon, 11 Apr 2011 19:32:07 +0000 (19:32 +0000)]
1.18.0 - fixed make.shared abort issue
westcott [Mon, 11 Apr 2011 17:46:27 +0000 (17:46 +0000)]
1.18.0
westcott [Mon, 11 Apr 2011 17:38:56 +0000 (17:38 +0000)]
1.18.0
pschloss [Mon, 11 Apr 2011 17:29:28 +0000 (17:29 +0000)]
pat's fixes to pca command
westcott [Mon, 11 Apr 2011 12:17:20 +0000 (12:17 +0000)]
fixed sub.sample groups bug
pschloss [Fri, 8 Apr 2011 17:45:10 +0000 (17:45 +0000)]
a few meaningless changes that are commented out
westcott [Fri, 8 Apr 2011 15:40:16 +0000 (15:40 +0000)]
fixed sub.sample so that it will eliminate samples with abundances that are less than the size selected
westcott [Fri, 8 Apr 2011 13:30:14 +0000 (13:30 +0000)]
fixing bugs while testing
westcott [Thu, 7 Apr 2011 15:12:08 +0000 (15:12 +0000)]
fixed bug with tree reading
westcott [Wed, 6 Apr 2011 17:34:11 +0000 (17:34 +0000)]
changes while setting up test files
westcott [Wed, 6 Apr 2011 16:20:43 +0000 (16:20 +0000)]
added getCommandInfoCommand for gui
westcott [Wed, 6 Apr 2011 13:27:11 +0000 (13:27 +0000)]
added commandParameter class
westcott [Wed, 6 Apr 2011 13:22:57 +0000 (13:22 +0000)]
removed read.dist, read.otu, read.tree and globaldata. added current to defaults for required parameters, changed virtual functions for the command class
westcott [Mon, 4 Apr 2011 14:36:21 +0000 (14:36 +0000)]
sped up the remove.seqs and remove.lineage and get.seqs and get.lineage. fixed bug with nast removeextrgaps
westcott [Wed, 30 Mar 2011 13:33:57 +0000 (13:33 +0000)]
fixed problem with sffinfo that caused a file mismatch when the trimming trimmed the entire sequence. in trim.seqs checked for blank primer name to remove extra .
pschloss [Wed, 30 Mar 2011 11:33:08 +0000 (11:33 +0000)]
made dups=T default in get.seqs
pschloss [Tue, 29 Mar 2011 03:03:59 +0000 (03:03 +0000)]
removed some of the warning output from chimera.slayer
pschloss [Wed, 23 Mar 2011 12:07:55 +0000 (12:07 +0000)]
small mod to chimerarefseq.cpp
westcott [Tue, 22 Mar 2011 13:23:30 +0000 (13:23 +0000)]
fixed trim.seqs group counts by adding back in the primer group
westcott [Tue, 22 Mar 2011 12:43:51 +0000 (12:43 +0000)]
working on pca
westcott [Tue, 22 Mar 2011 12:43:51 +0000 (12:43 +0000)]
working on pca
westcott [Tue, 22 Mar 2011 11:43:48 +0000 (11:43 +0000)]
fixed clearcut version bug, added group count output to get.groups and remove.groups
westcott [Tue, 22 Mar 2011 11:38:42 +0000 (11:38 +0000)]
fixed clearcut version bug, added group count output to get.groups and remove.groups
pschloss [Mon, 21 Mar 2011 11:28:49 +0000 (11:28 +0000)]
random chagnes from pat
westcott [Mon, 21 Mar 2011 11:08:28 +0000 (11:08 +0000)]
fixed get.lienage and remove.lineage bug with confidence scores that are floats. fixed bug with pairwiase.seqs that was caused by using nast.
westcott [Wed, 16 Mar 2011 18:47:41 +0000 (18:47 +0000)]
fixed catchall "clunky" names
westcott [Wed, 16 Mar 2011 17:59:01 +0000 (17:59 +0000)]
fixed the bug that caused mothur to choke on other commands after running catchall with a shared file
westcott [Wed, 16 Mar 2011 17:14:04 +0000 (17:14 +0000)]
added set.current and get.current commands and modified existing commands to update the current files with their output files.
westcott [Tue, 15 Mar 2011 19:40:48 +0000 (19:40 +0000)]
adding current file class
westcott [Tue, 15 Mar 2011 18:14:35 +0000 (18:14 +0000)]
adding current file class
westcott [Fri, 11 Mar 2011 18:00:43 +0000 (18:00 +0000)]
sped up align.seqs appending of files
pschloss [Fri, 11 Mar 2011 17:25:49 +0000 (17:25 +0000)]
some more mods to shh.seqs
westcott [Fri, 11 Mar 2011 16:55:27 +0000 (16:55 +0000)]
added summary outputs for align.check
westcott [Fri, 11 Mar 2011 15:54:35 +0000 (15:54 +0000)]
added namefile to align.check and added seqs from namefile to optimizing piece of screen.seqs
westcott [Fri, 11 Mar 2011 14:09:47 +0000 (14:09 +0000)]
added namefile to summary.seqs
pschloss [Fri, 11 Mar 2011 13:28:33 +0000 (13:28 +0000)]
some changes to trim.flows
pschloss [Mon, 7 Mar 2011 22:44:36 +0000 (22:44 +0000)]
removed some couts from qualityscores.cpp
pschloss [Mon, 7 Mar 2011 22:39:32 +0000 (22:39 +0000)]
fix trim.seqs / qualscores bug
westcott [Mon, 7 Mar 2011 22:30:47 +0000 (22:30 +0000)]
trim.seqs fix
westcott [Fri, 4 Mar 2011 15:45:49 +0000 (15:45 +0000)]
worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNames, added sequence group counts
westcott [Fri, 4 Mar 2011 15:45:49 +0000 (15:45 +0000)]
worked on trim.seqs - added in the groupfiles for allfiles=t, cleaned up the outputNames, added sequence group counts
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
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