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git.donarmstrong.com Git - mothur.git/log
westcott [Tue, 24 Feb 2009 13:01:38 +0000 (13:01 +0000)]
parsimony fix
westcott [Mon, 23 Feb 2009 20:09:07 +0000 (20:09 +0000)]
fixed parsimony for groups
westcott [Mon, 23 Feb 2009 17:48:26 +0000 (17:48 +0000)]
fixed parsimony for groups
westcott [Mon, 23 Feb 2009 13:55:04 +0000 (13:55 +0000)]
fixed unweighted calculator
westcott [Fri, 20 Feb 2009 17:34:55 +0000 (17:34 +0000)]
fixed unweighted calculator
westcott [Thu, 19 Feb 2009 14:45:41 +0000 (14:45 +0000)]
added mothur.h and fixed includes in many files
westcott [Thu, 19 Feb 2009 13:51:33 +0000 (13:51 +0000)]
fixed linking error in collect, collectshared, and errorcheckor
westcott [Wed, 18 Feb 2009 23:58:22 +0000 (23:58 +0000)]
Johns fix
ryabin [Wed, 18 Feb 2009 19:42:11 +0000 (19:42 +0000)]
Added get.line command.
Added get.label command.
Added get.group command.
Added parameter and parameter value error checking.
Modified ace to allow changing the abund variable.
Made it so you don't need a space after the comma when entering parameters.
Added error checking for invalid labels.
Added a new convert method that tests if a given string can be converted into an int.
ryabin [Wed, 18 Feb 2009 19:28:34 +0000 (19:28 +0000)]
Added get.line command.
Added get.label command.
Added get.group command.
Added parameter and parameter value error checking.
Modified ace to allow changing the abund variable.
Made it so you don't need a space after the comma when entering parameters.
Added error checking for invalid labels.
Added a new convert method that tests if a given string can be converted into an int.
westcott [Wed, 18 Feb 2009 18:51:16 +0000 (18:51 +0000)]
parsimony command now uses groups, fixed bug with unweighted groups
westcott [Wed, 18 Feb 2009 18:28:27 +0000 (18:28 +0000)]
parsimony command now uses groups, fixed bug with unweighted groups
westcott [Wed, 18 Feb 2009 17:09:09 +0000 (17:09 +0000)]
changed unweighted and weighted score cumulatives to be that score or higher instead of lower.
pschloss [Wed, 18 Feb 2009 15:56:06 +0000 (15:56 +0000)]
fixed bug in read.tree
westcott [Wed, 18 Feb 2009 15:34:00 +0000 (15:34 +0000)]
fixed bug in fastmap readFastaFile so that if there is a blank line inbetween the sequences it still runs.
westcott [Wed, 18 Feb 2009 15:11:01 +0000 (15:11 +0000)]
minor bugs fixes and added line and label options to read.otu's parselist and shared commands.
westcott [Fri, 13 Feb 2009 17:29:04 +0000 (17:29 +0000)]
minor error checking fixes
westcott [Fri, 13 Feb 2009 16:49:49 +0000 (16:49 +0000)]
added read.shared, broke up globaldata a bit
westcott [Thu, 12 Feb 2009 14:52:49 +0000 (14:52 +0000)]
fixed bug with displaying info for collect.shared() and summary.shared().
westcott [Wed, 11 Feb 2009 18:14:23 +0000 (18:14 +0000)]
added errorchecking and help info on new unifrac and treeclimber code
westcott [Wed, 11 Feb 2009 15:42:13 +0000 (15:42 +0000)]
adding treeclimber and unifrac pieces
pschloss [Fri, 30 Jan 2009 12:49:01 +0000 (12:49 +0000)]
When Pat tried to compile mothur in Ubuntu linux, there were a number of minor problems that needed to be fixed in the code
westcott [Thu, 29 Jan 2009 15:01:56 +0000 (15:01 +0000)]
changed all files to be relative to project instead of relative to enclosing group
westcott [Thu, 29 Jan 2009 14:36:15 +0000 (14:36 +0000)]
rarefaction.shared() fixed bug
westcott [Wed, 28 Jan 2009 17:28:11 +0000 (17:28 +0000)]
fixed line and label bug.
westcott [Wed, 28 Jan 2009 16:30:46 +0000 (16:30 +0000)]
updated help
westcott [Wed, 28 Jan 2009 15:02:56 +0000 (15:02 +0000)]
rarefaction default bug
westcott [Wed, 28 Jan 2009 14:46:58 +0000 (14:46 +0000)]
fixed parameter issues
westcott [Wed, 28 Jan 2009 14:38:16 +0000 (14:38 +0000)]
collect.single bug in readphil.
pschloss [Wed, 28 Jan 2009 14:04:05 +0000 (14:04 +0000)]
I've changed the listfile, sabundfile, etc. option handles to not need the "file" part - pat
westcott [Mon, 26 Jan 2009 15:31:55 +0000 (15:31 +0000)]
fixed summary.shared bug and set jumble default to 1.
westcott [Fri, 23 Jan 2009 13:06:57 +0000 (13:06 +0000)]
fixed bug in sharedcommand and parselistcommand and changed file extension of sorensonabund.
westcott [Thu, 22 Jan 2009 16:49:25 +0000 (16:49 +0000)]
finishing the container classes, combining read.otu and read.list commands. some cosmetic fixes.
westcott [Wed, 21 Jan 2009 16:12:57 +0000 (16:12 +0000)]
deconvolute command
westcott [Tue, 20 Jan 2009 18:33:14 +0000 (18:33 +0000)]
changed read.shared to read.list and incorporated the shared and parselist commands into it.
pschloss [Sat, 17 Jan 2009 00:38:06 +0000 (00:38 +0000)]
Updated the project setting parameters
westcott [Fri, 16 Jan 2009 22:17:34 +0000 (22:17 +0000)]
Initial revision
pschloss [Thu, 15 Jan 2009 17:36:50 +0000 (17:36 +0000)]
Initial revision