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git.donarmstrong.com Git - mothur.git/log
westcott [Tue, 24 Nov 2009 12:41:40 +0000 (12:41 +0000)]
fixed bug in hcluster command
westcott [Mon, 23 Nov 2009 19:24:47 +0000 (19:24 +0000)]
edited taxonomy equalizer to fix bug with windows
westcott [Mon, 23 Nov 2009 18:57:03 +0000 (18:57 +0000)]
updated phylotype command
westcott [Mon, 23 Nov 2009 18:40:54 +0000 (18:40 +0000)]
changed label outputs for phylotype command
westcott [Mon, 23 Nov 2009 17:27:06 +0000 (17:27 +0000)]
added phylotype command which reads a taxonomy file and creates a .list, .rabund and .sabund file.
westcott [Thu, 19 Nov 2009 20:04:04 +0000 (20:04 +0000)]
fixed bug in libshuff
westcott [Tue, 17 Nov 2009 17:14:58 +0000 (17:14 +0000)]
final fixes for 1.7
westcott [Fri, 13 Nov 2009 16:01:14 +0000 (16:01 +0000)]
finished work on classify.seqs bayesian method and various bug fixes
westcott [Thu, 5 Nov 2009 14:40:15 +0000 (14:40 +0000)]
started work on classify.seqs command. changed the database class so that it does not store the template sequences. created alignmentDB class that stores template seqs and uses database class for searching. made changes to aligncommand and chimeracheckrdp to reflect the changes to database class.
westcott [Mon, 2 Nov 2009 15:43:43 +0000 (15:43 +0000)]
added groups option to read.otu, added qtrim option to trim.seqs, fixed bug in get.oturep that started bin numbers at 0, finished work on hcluster command.
westcott [Thu, 29 Oct 2009 18:17:36 +0000 (18:17 +0000)]
fixed bug with hcluster
westcott [Thu, 29 Oct 2009 13:56:37 +0000 (13:56 +0000)]
added hcluster command and fixed some bugs, namely one with smart distancing.
westcott [Mon, 12 Oct 2009 21:26:13 +0000 (21:26 +0000)]
finished chimeraslayer method and added get.listcount command
westcott [Tue, 29 Sep 2009 16:05:10 +0000 (16:05 +0000)]
working on chimeraslayer and found bug in shared command.
westcott [Mon, 28 Sep 2009 14:31:48 +0000 (14:31 +0000)]
started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstructor
westcott [Wed, 23 Sep 2009 13:32:40 +0000 (13:32 +0000)]
added get.sharedotu command
westcott [Tue, 22 Sep 2009 14:16:08 +0000 (14:16 +0000)]
removed line option
westcott [Mon, 21 Sep 2009 13:19:02 +0000 (13:19 +0000)]
align.check command added
westcott [Fri, 18 Sep 2009 17:38:21 +0000 (17:38 +0000)]
adding more error checking for list and group files. outputs missing.names or missing.group if you have files with different number of sequences in them
westcott [Fri, 18 Sep 2009 12:19:52 +0000 (12:19 +0000)]
removing extra file output from pintail
westcott [Thu, 17 Sep 2009 13:48:20 +0000 (13:48 +0000)]
added check for blank files in openInputFile, add check for groupfiles that contain more seqs than the list files in sharedcommand
westcott [Tue, 15 Sep 2009 17:43:32 +0000 (17:43 +0000)]
fixed some issues while testing 1.6
westcott [Mon, 14 Sep 2009 15:01:48 +0000 (15:01 +0000)]
added help to chimera.seqs
westcott [Fri, 11 Sep 2009 16:28:24 +0000 (16:28 +0000)]
chimeracheck method added
westcott [Wed, 9 Sep 2009 20:20:23 +0000 (20:20 +0000)]
continued work on chimeras and fixed bug in trim.seqs and reverse.seqs that was due to the fact that we changed the sequence class so that all seqs now have an aligned version. that change was made to fix another bug.
westcott [Tue, 8 Sep 2009 13:53:16 +0000 (13:53 +0000)]
finished with ccode, returned bellerophon to last save before move, cleaned up pintails outputs
westcott [Fri, 4 Sep 2009 16:01:17 +0000 (16:01 +0000)]
changed reporting in ccode to only report those who are found to be chimeric by all three tests, also fixed issue with the masking
westcott [Fri, 4 Sep 2009 15:06:54 +0000 (15:06 +0000)]
ccode working - still need to paralellize
westcott [Wed, 2 Sep 2009 09:50:25 +0000 (09:50 +0000)]
updated pats contact and mothur header info
westcott [Tue, 1 Sep 2009 19:16:29 +0000 (19:16 +0000)]
changed raredisplay to use vectors instead of files
westcott [Tue, 1 Sep 2009 12:17:14 +0000 (12:17 +0000)]
added more descriptive error messages to sharedlist
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
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