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git.donarmstrong.com Git - mothur.git/log
westcott [Mon, 31 Aug 2009 14:33:57 +0000 (14:33 +0000)]
checking in chimera files in progress after move to michigan
westcott [Thu, 13 Aug 2009 14:36:07 +0000 (14:36 +0000)]
last changes before move
westcott [Thu, 13 Aug 2009 14:01:10 +0000 (14:01 +0000)]
last changes before move
westcott [Wed, 12 Aug 2009 16:34:29 +0000 (16:34 +0000)]
removing mallard
westcott [Tue, 11 Aug 2009 18:08:37 +0000 (18:08 +0000)]
chimera.seqs pintail is working.
pschloss [Mon, 10 Aug 2009 16:21:39 +0000 (16:21 +0000)]
mothur-v.1.5.0
westcott [Thu, 6 Aug 2009 16:12:17 +0000 (16:12 +0000)]
This is 1.5.
westcott [Thu, 6 Aug 2009 15:14:39 +0000 (15:14 +0000)]
bugs fixes while testing for 1.5 release
westcott [Wed, 5 Aug 2009 22:25:58 +0000 (22:25 +0000)]
bugs fixes while testing for 1.5 release
westcott [Wed, 5 Aug 2009 18:32:19 +0000 (18:32 +0000)]
bugs fixes while testing for 1.5 release
westcott [Mon, 3 Aug 2009 20:08:43 +0000 (20:08 +0000)]
bugs for 1.5
westcott [Mon, 3 Aug 2009 12:17:33 +0000 (12:17 +0000)]
bugs for 1.5
westcott [Sun, 2 Aug 2009 20:55:29 +0000 (20:55 +0000)]
bugs fixes while testing for 1.5 release
westcott [Sat, 1 Aug 2009 21:28:33 +0000 (21:28 +0000)]
bugs fixes while testing for 1.5 release
westcott [Thu, 30 Jul 2009 19:08:54 +0000 (19:08 +0000)]
working on chimeras
pschloss [Thu, 30 Jul 2009 15:27:29 +0000 (15:27 +0000)]
pat's changes after generating wiki pages for 1.5
westcott [Thu, 30 Jul 2009 12:03:32 +0000 (12:03 +0000)]
Thallinger changes to cluster command.
pschloss [Thu, 30 Jul 2009 11:25:41 +0000 (11:25 +0000)]
pat's edits prior to v.1.5
westcott [Tue, 28 Jul 2009 17:17:20 +0000 (17:17 +0000)]
working on chimeras
westcott [Sun, 26 Jul 2009 23:56:29 +0000 (23:56 +0000)]
fixed bug with aligner in database class, worked on chimeras
westcott [Wed, 22 Jul 2009 18:58:12 +0000 (18:58 +0000)]
worked on chimeras
westcott [Wed, 22 Jul 2009 11:35:33 +0000 (11:35 +0000)]
changed sequence class so that when constructor is called aligned and unaligned values are filled, also worked on chimeras
westcott [Mon, 20 Jul 2009 19:33:56 +0000 (19:33 +0000)]
fixed bugs in venn and aligner
westcott [Tue, 14 Jul 2009 21:24:03 +0000 (21:24 +0000)]
*** empty log message ***
westcott [Fri, 10 Jul 2009 15:53:50 +0000 (15:53 +0000)]
added sorted option to get.rabund command
westcott [Thu, 9 Jul 2009 13:10:26 +0000 (13:10 +0000)]
added getline function to mothur and modified places where we use getline to use this new function.
westcott [Wed, 8 Jul 2009 17:06:42 +0000 (17:06 +0000)]
added stricter compilation requirements and fixed resulting errors
westcott [Wed, 8 Jul 2009 16:23:14 +0000 (16:23 +0000)]
added system command
westcott [Wed, 8 Jul 2009 15:40:10 +0000 (15:40 +0000)]
added remove.seqs command
westcott [Wed, 8 Jul 2009 14:50:50 +0000 (14:50 +0000)]
added get.seqs command
westcott [Wed, 8 Jul 2009 13:31:28 +0000 (13:31 +0000)]
added list.seqs command
westcott [Mon, 6 Jul 2009 12:41:02 +0000 (12:41 +0000)]
fixed bug in sequencedb read for windows users and substr error in trim.seqs
westcott [Thu, 2 Jul 2009 15:11:04 +0000 (15:11 +0000)]
made changes to concensus to find a better tree. also fixed minor bug in venn with 4 groups
westcott [Mon, 29 Jun 2009 14:52:33 +0000 (14:52 +0000)]
fixed misspelling on consensus
westcott [Mon, 29 Jun 2009 14:43:21 +0000 (14:43 +0000)]
fixed bug in bootstrap command that was caused by globaldata's breakup, and made concensus command part of bootstrap.shared
westcott [Mon, 29 Jun 2009 13:01:52 +0000 (13:01 +0000)]
modified read.otu and shared command
westcott [Thu, 25 Jun 2009 18:33:56 +0000 (18:33 +0000)]
added logfile feature
pschloss [Tue, 23 Jun 2009 17:09:16 +0000 (17:09 +0000)]
mothur v.1.4.1
westcott [Tue, 23 Jun 2009 15:36:46 +0000 (15:36 +0000)]
changed how we do "smart" distancing
westcott [Mon, 22 Jun 2009 18:47:04 +0000 (18:47 +0000)]
worked on parselist and shared commands, removing memory leaks and allowing any number of groups to be used by parselist.
pschloss [Sun, 21 Jun 2009 13:47:29 +0000 (13:47 +0000)]
This is v.1.4.0
westcott [Fri, 19 Jun 2009 18:15:30 +0000 (18:15 +0000)]
version 1.4
westcott [Fri, 19 Jun 2009 17:15:00 +0000 (17:15 +0000)]
version working on mac with .tellg changed to unget for windows
westcott [Thu, 18 Jun 2009 16:05:46 +0000 (16:05 +0000)]
fixed some bugs
pschloss [Thu, 18 Jun 2009 12:20:36 +0000 (12:20 +0000)]
added an alignreport option to screen seqs
pschloss [Tue, 16 Jun 2009 21:18:51 +0000 (21:18 +0000)]
a few minor things - pds
westcott [Tue, 16 Jun 2009 19:01:09 +0000 (19:01 +0000)]
fixed some bugs and added scriptengine
westcott [Mon, 15 Jun 2009 19:13:51 +0000 (19:13 +0000)]
fixing minor bugs
westcott [Mon, 15 Jun 2009 12:08:39 +0000 (12:08 +0000)]
removed validcommands and put its checking in commandfactory.
pschloss [Sun, 14 Jun 2009 20:59:57 +0000 (20:59 +0000)]
merged pat's trim seqs edits with sarah's major overhaul of global data; also added merge.files
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.