]>
git.donarmstrong.com Git - mothur.git/log
westcott [Fri, 12 Jun 2009 19:41:27 +0000 (19:41 +0000)]
broke up globaldata and moved error checking and help into commands
westcott [Mon, 8 Jun 2009 16:40:33 +0000 (16:40 +0000)]
got rid of extra temp files in dist.seqs
westcott [Mon, 8 Jun 2009 16:22:46 +0000 (16:22 +0000)]
added help for heatmap.sim
westcott [Mon, 8 Jun 2009 16:14:18 +0000 (16:14 +0000)]
added heatmap.sim command and changed heatmap to heatmap.bin
pschloss [Mon, 8 Jun 2009 15:51:58 +0000 (15:51 +0000)]
fixed how seq.dists divides the matrix for multiple processors
pschloss [Mon, 8 Jun 2009 14:34:08 +0000 (14:34 +0000)]
added some features to trim.seqs
westcott [Mon, 8 Jun 2009 13:16:54 +0000 (13:16 +0000)]
dist.seqs can now use n processors, and only outputs the phylip formatted distance matrix if the user sets phylip=t
pschloss [Sun, 7 Jun 2009 02:23:44 +0000 (02:23 +0000)]
modified trim.seqs command
pschloss [Sat, 6 Jun 2009 23:55:02 +0000 (23:55 +0000)]
added trim.seqs command
pschloss [Sat, 6 Jun 2009 10:35:06 +0000 (10:35 +0000)]
added reverse.seqs command
westcott [Fri, 5 Jun 2009 13:05:11 +0000 (13:05 +0000)]
line and label no longer persist between commands. Added phylip formated output to dist.seqs command.
pschloss [Thu, 4 Jun 2009 17:33:37 +0000 (17:33 +0000)]
remove some files
westcott [Thu, 4 Jun 2009 17:03:32 +0000 (17:03 +0000)]
removed readseqs, readfasta, readnexus, readclustal, readseqsphylip and updated sequencedb to be a container that can read from a file.
pschloss [Thu, 4 Jun 2009 15:32:33 +0000 (15:32 +0000)]
modified filter.seqs to not store all seqs in memory but to read off disc
pschloss [Thu, 4 Jun 2009 14:26:19 +0000 (14:26 +0000)]
*** empty log message ***
westcott [Thu, 4 Jun 2009 14:10:53 +0000 (14:10 +0000)]
fixed some bugs
pschloss [Thu, 4 Jun 2009 13:59:25 +0000 (13:59 +0000)]
pat's edits of screen.seqs and summary.seqs
pschloss [Wed, 3 Jun 2009 18:39:56 +0000 (18:39 +0000)]
fixed a bug in calculating the # of ambig bases
pschloss [Wed, 3 Jun 2009 18:21:39 +0000 (18:21 +0000)]
added screen.seqs command - pds
westcott [Wed, 3 Jun 2009 12:37:21 +0000 (12:37 +0000)]
added get.rabund and get.sabund command and fixed bug introduced by line by line optimization
pschloss [Wed, 3 Jun 2009 01:39:31 +0000 (01:39 +0000)]
addition of summary.seq command [pds]
westcott [Tue, 2 Jun 2009 16:10:12 +0000 (16:10 +0000)]
allow user to input quit instead of quit()
westcott [Tue, 2 Jun 2009 16:02:18 +0000 (16:02 +0000)]
added smart distance feature and optimized all commands using line by line processing
westcott [Mon, 1 Jun 2009 13:09:19 +0000 (13:09 +0000)]
fixed bug for windows users with read.dist
westcott [Mon, 1 Jun 2009 12:08:29 +0000 (12:08 +0000)]
*** empty log message ***
westcott [Wed, 27 May 2009 23:17:57 +0000 (23:17 +0000)]
fixed multiple bugs for 1.4 release
modified tree.shared to allow using a distance file
pschloss [Sun, 24 May 2009 16:39:16 +0000 (16:39 +0000)]
This contains Pat's bug fixes and updates. It represents mothur v.1.3.0
westcott [Fri, 22 May 2009 19:16:27 +0000 (19:16 +0000)]
changed defaults for filter.seqs()
westcott [Fri, 22 May 2009 18:48:55 +0000 (18:48 +0000)]
changed defaults in allign.seqs command
westcott [Thu, 21 May 2009 18:42:57 +0000 (18:42 +0000)]
fixed bugs
westcott [Thu, 21 May 2009 16:45:22 +0000 (16:45 +0000)]
modified bin.seqs and get.oturep commands to include use of a groupfile if provided and removed get.repseqs command.
westcott [Thu, 21 May 2009 14:44:28 +0000 (14:44 +0000)]
added ability to put # in front of any line in the batch file you don't want to use
westcott [Thu, 21 May 2009 14:13:47 +0000 (14:13 +0000)]
fixed Thomas' calculators
westcott [Thu, 21 May 2009 13:18:32 +0000 (13:18 +0000)]
fixed blast code path problem
westcott [Thu, 21 May 2009 12:35:43 +0000 (12:35 +0000)]
added dist.shared command
westcott [Wed, 20 May 2009 16:34:26 +0000 (16:34 +0000)]
added get.repseqs command, started matrix output command
westcott [Mon, 18 May 2009 20:02:15 +0000 (20:02 +0000)]
added shen calculator
westcott [Mon, 18 May 2009 19:56:29 +0000 (19:56 +0000)]
added shen calculator
westcott [Mon, 18 May 2009 18:56:27 +0000 (18:56 +0000)]
added help for alignment code and thomas' calcs to project
westcott [Mon, 18 May 2009 18:24:13 +0000 (18:24 +0000)]
added boneh, efron, and solow calculators
westcott [Mon, 18 May 2009 17:37:53 +0000 (17:37 +0000)]
added alignment code
westcott [Fri, 15 May 2009 16:45:37 +0000 (16:45 +0000)]
fixed if defined in dist.seqs command
westcott [Fri, 15 May 2009 14:39:11 +0000 (14:39 +0000)]
fixed memory leak in collect.shared()
westcott [Fri, 15 May 2009 13:55:53 +0000 (13:55 +0000)]
speed up rarefaction.shared
westcott [Fri, 15 May 2009 12:33:58 +0000 (12:33 +0000)]
fixed bug in heatmap
westcott [Thu, 14 May 2009 15:43:23 +0000 (15:43 +0000)]
fixed memory leak in rarefact
westcott [Thu, 14 May 2009 13:22:38 +0000 (13:22 +0000)]
fixed bug in venn command
westcott [Wed, 13 May 2009 19:24:31 +0000 (19:24 +0000)]
changed name of distance command to dist.seqs
westcott [Wed, 13 May 2009 18:35:14 +0000 (18:35 +0000)]
changed all shared commands so that they read the shared file generated by the read.otu instead of the list and group combo.
westcott [Wed, 13 May 2009 15:19:07 +0000 (15:19 +0000)]
fixed bug with getting sharedrabunds for venn, heatmap and tree.shared commands, speeding them up a bit.
westcott [Tue, 12 May 2009 16:31:52 +0000 (16:31 +0000)]
added distance command and filterseqs
westcott [Fri, 8 May 2009 16:52:01 +0000 (16:52 +0000)]
altered venn command to make use of sharedchao for any number of groups, fixed windows users bug with deconvolute command. Began adding distance command.
ryabin [Fri, 8 May 2009 16:26:50 +0000 (16:26 +0000)]
filterseqscommand added
westcott [Thu, 7 May 2009 15:47:53 +0000 (15:47 +0000)]
fixed concensus command and modified tree class so you can print labels on trees
ryabin [Mon, 4 May 2009 22:20:46 +0000 (22:20 +0000)]
*** empty log message ***
westcott [Mon, 4 May 2009 20:19:18 +0000 (20:19 +0000)]
fixed xp user bug with rarefact commands and cluster error checking
westcott [Mon, 4 May 2009 13:45:55 +0000 (13:45 +0000)]
added concensus command and updated calcs
westcott [Mon, 4 May 2009 13:35:25 +0000 (13:35 +0000)]
added concensus command and updated calcs
westcott [Mon, 4 May 2009 12:33:27 +0000 (12:33 +0000)]
added concensus command
pschloss [Fri, 24 Apr 2009 21:58:56 +0000 (21:58 +0000)]
This is mothur v 1.2.0 - the April ~24, 2009 release
pschloss [Thu, 23 Apr 2009 20:01:31 +0000 (20:01 +0000)]
more calculator edits and added coverage and whittaker
pschloss [Wed, 22 Apr 2009 22:09:36 +0000 (22:09 +0000)]
modified some calculators and other stuff - pds
westcott [Wed, 22 Apr 2009 15:47:04 +0000 (15:47 +0000)]
changed heatmap and venn command to use vector of sharedrabunds instead of order. Added functions to readotu, inputdata, sharedordervector, sharedlistvector to support that change, as well as modified sharedutilities setGroups.
westcott [Tue, 21 Apr 2009 18:29:12 +0000 (18:29 +0000)]
broke apart read matrix file
westcott [Tue, 21 Apr 2009 15:14:13 +0000 (15:14 +0000)]
fixed bug with get.oturep and fixed problem with errorcheckor that did not allow the user to read a phylip and then a column.
westcott [Tue, 21 Apr 2009 13:33:41 +0000 (13:33 +0000)]
fixed bug with parsimony(groups=all) and unifrac.unweighted(groups=all)
westcott [Tue, 21 Apr 2009 12:51:54 +0000 (12:51 +0000)]
fixed bug in venn command which caused error when user used more than one distance level.
pschloss [Mon, 20 Apr 2009 20:37:11 +0000 (20:37 +0000)]
pds fixes of heatmap and some other minor stuff
westcott [Fri, 17 Apr 2009 15:43:01 +0000 (15:43 +0000)]
added bootstrap.shared command and fixed some bugs with heatmap
westcott [Tue, 14 Apr 2009 17:16:14 +0000 (17:16 +0000)]
removed "shared" from some of the calculator names and classes
pschloss [Tue, 14 Apr 2009 14:14:38 +0000 (14:14 +0000)]
*** empty log message ***
westcott [Tue, 14 Apr 2009 13:17:08 +0000 (13:17 +0000)]
added log10 and log2 scalers for heatmap
westcott [Tue, 14 Apr 2009 12:04:57 +0000 (12:04 +0000)]
started shared utilities, updates to venn and heatmap added tree.groups command
westcott [Wed, 8 Apr 2009 15:23:31 +0000 (15:23 +0000)]
fixed bug in read.tree updates help and validparameters strings, added ability for user to leave names out of the groupfile or add extra names with read.tree.
westcott [Mon, 6 Apr 2009 18:21:45 +0000 (18:21 +0000)]
added get.oturep command
westcott [Mon, 6 Apr 2009 14:48:16 +0000 (14:48 +0000)]
fixed memory leak in parsimony calculator and added progress bars to parsimony and unifrac.weighted commands. also added bin.seqs command.
westcott [Fri, 3 Apr 2009 13:36:40 +0000 (13:36 +0000)]
venn command with up to 4 groups using sharedsobs, sharedchao and sharedace estimators for shared as well as sobs, chao, ace and jackknife for singles.
westcott [Thu, 2 Apr 2009 15:21:36 +0000 (15:21 +0000)]
venn command with up to 4 groups
westcott [Tue, 31 Mar 2009 13:40:32 +0000 (13:40 +0000)]
started venn command
ryabin [Mon, 30 Mar 2009 20:18:37 +0000 (20:18 +0000)]
Fixed validParameter() method so line parameter can use dashes without breaking the covertTest() method.
westcott [Mon, 30 Mar 2009 13:58:26 +0000 (13:58 +0000)]
made sorting optional but sort by default, in case the user wants to see the heatmap representation of their inputfile.
westcott [Mon, 30 Mar 2009 13:31:37 +0000 (13:31 +0000)]
added sort to heatmap to put shared otus at the top and updated some error checking
westcott [Fri, 27 Mar 2009 20:22:41 +0000 (20:22 +0000)]
fixed reference issue
westcott [Fri, 27 Mar 2009 20:09:47 +0000 (20:09 +0000)]
added heatmap command
westcott [Fri, 27 Mar 2009 20:02:04 +0000 (20:02 +0000)]
added heatmap command
ryabin [Fri, 27 Mar 2009 19:25:26 +0000 (19:25 +0000)]
added the Calculators Thomas made in the fall. Added parameter and command error checking.
ryabin [Fri, 27 Mar 2009 19:25:25 +0000 (19:25 +0000)]
added the Calculators Thomas made in the fall. Added parameter and command error checking.
westcott [Thu, 26 Mar 2009 14:43:41 +0000 (14:43 +0000)]
heatmap
westcott [Wed, 25 Mar 2009 14:37:21 +0000 (14:37 +0000)]
started heatmap command
westcott [Tue, 24 Mar 2009 15:11:00 +0000 (15:11 +0000)]
added sharedbraycurtis, sharedmorisirahorn, sharedkulczynski, sharedkulczynskicody and sharedlennon calculators.
westcott [Mon, 23 Mar 2009 18:34:44 +0000 (18:34 +0000)]
added sharedochiai and sharedanderberg calculators
westcott [Mon, 23 Mar 2009 17:23:57 +0000 (17:23 +0000)]
fixed libshuff signif. values
westcott [Mon, 23 Mar 2009 14:51:32 +0000 (14:51 +0000)]
put back no command and worked on libshuff
westcott [Fri, 20 Mar 2009 18:21:06 +0000 (18:21 +0000)]
removed no command because it is never called now that we error check for the command name.
westcott [Fri, 20 Mar 2009 16:14:10 +0000 (16:14 +0000)]
documentation
westcott [Thu, 19 Mar 2009 17:48:18 +0000 (17:48 +0000)]
fixed memory leak globaldata container structures, gTreemap, ginput, gorder, gSharedList, gMatrix.
westcott [Thu, 19 Mar 2009 17:04:49 +0000 (17:04 +0000)]
fixed memory leak of groupmap in reads
westcott [Thu, 19 Mar 2009 15:25:06 +0000 (15:25 +0000)]
updated errorchecking so it checks if the parameter is valid for the command.
westcott [Thu, 19 Mar 2009 14:02:15 +0000 (14:02 +0000)]
libshuff and updated help to include libshuff and modifications to read.dist.
westcott [Wed, 18 Mar 2009 16:05:36 +0000 (16:05 +0000)]
working on libshuff