]>
git.donarmstrong.com Git - mothur.git/log
westcott [Fri, 18 Jun 2010 17:50:19 +0000 (17:50 +0000)]
fixed problem with trim.seqs writing over files if barcodes belonged to the same group
westcott [Fri, 18 Jun 2010 11:37:36 +0000 (11:37 +0000)]
fixed problem with chimera.slayer realigner
westcott [Thu, 17 Jun 2010 14:08:24 +0000 (14:08 +0000)]
changes for 1.11
westcott [Thu, 17 Jun 2010 14:05:18 +0000 (14:05 +0000)]
changes while testing 1.11
pschloss [Thu, 17 Jun 2010 12:57:40 +0000 (12:57 +0000)]
made a small mod to the alignment parameters in trim.seqs
westcott [Wed, 16 Jun 2010 13:59:57 +0000 (13:59 +0000)]
fixes while testing
westcott [Tue, 15 Jun 2010 13:59:28 +0000 (13:59 +0000)]
changed how we count sequences in a fastafile to allow for '>' in sequence names
westcott [Tue, 15 Jun 2010 13:50:04 +0000 (13:50 +0000)]
changed how we count sequences in a fastafile to allow for '>' in sequence names
westcott [Tue, 15 Jun 2010 12:05:46 +0000 (12:05 +0000)]
final commit before testing 1.11
westcott [Mon, 14 Jun 2010 18:28:12 +0000 (18:28 +0000)]
modified chop.seqs
westcott [Mon, 14 Jun 2010 17:06:03 +0000 (17:06 +0000)]
fixed read.tree so that it can read trees generated by fasttree
westcott [Mon, 14 Jun 2010 14:30:17 +0000 (14:30 +0000)]
added fasta method to cluster.split
westcott [Mon, 14 Jun 2010 14:01:32 +0000 (14:01 +0000)]
fixed bug in cluster.split
westcott [Mon, 14 Jun 2010 12:13:19 +0000 (12:13 +0000)]
fixed pintail bug
pschloss [Sat, 12 Jun 2010 23:28:24 +0000 (23:28 +0000)]
pat's mod to trim.seqs
westcott [Fri, 11 Jun 2010 15:37:05 +0000 (15:37 +0000)]
fixed bug in cluster.split with classify method
westcott [Thu, 10 Jun 2010 17:53:15 +0000 (17:53 +0000)]
committing so I can work on the other machine
pschloss [Wed, 9 Jun 2010 17:00:29 +0000 (17:00 +0000)]
fixed bug in nast:removeextragaps
pschloss [Wed, 9 Jun 2010 14:51:50 +0000 (14:51 +0000)]
added weightedlinkage.cpp
westcott [Wed, 9 Jun 2010 13:53:28 +0000 (13:53 +0000)]
changes to blastdb to make filenames given to blast unique, changes to split.abund, fixed bugs in chimera.slayer realigner, optimized splitmatrix and modified cluster.split command.
westcott [Wed, 9 Jun 2010 12:07:11 +0000 (12:07 +0000)]
changes to blastdb to make filenames given to blast unique, changes to split.abund, fixed bugs in chimera.slayer realigner, optimized splitmatrix and modified cluster.split command.
westcott [Fri, 4 Jun 2010 18:01:04 +0000 (18:01 +0000)]
sped up splitting of distance file by 2.5 times by buffering the read and writes.
westcott [Thu, 3 Jun 2010 17:02:17 +0000 (17:02 +0000)]
fixed cluster.split command
westcott [Wed, 2 Jun 2010 15:23:36 +0000 (15:23 +0000)]
added sort parameter to get.otulist
westcott [Wed, 2 Jun 2010 15:00:10 +0000 (15:00 +0000)]
added taxonomy file to list of files list.seqs, get.seqs and remove.seqs can process
westcott [Wed, 2 Jun 2010 14:03:39 +0000 (14:03 +0000)]
added classify.otu command
westcott [Wed, 2 Jun 2010 14:03:39 +0000 (14:03 +0000)]
added classify.otu command
westcott [Tue, 1 Jun 2010 15:44:15 +0000 (15:44 +0000)]
changed the daughterLevels in classifiers summary file to reflect the classifications only the classifications in the query file.
westcott [Tue, 1 Jun 2010 13:52:48 +0000 (13:52 +0000)]
latest version
westcott [Fri, 28 May 2010 15:00:33 +0000 (15:00 +0000)]
finished cluster.split adding classify method.
westcott [Fri, 28 May 2010 12:20:41 +0000 (12:20 +0000)]
changed hard parameter in cluster commands
westcott [Thu, 27 May 2010 14:21:04 +0000 (14:21 +0000)]
fixed project
westcott [Thu, 27 May 2010 12:47:59 +0000 (12:47 +0000)]
changes to chop.seqs
pschloss [Wed, 26 May 2010 16:04:49 +0000 (16:04 +0000)]
fixed bugs with trim.seqs and bdiffs
westcott [Thu, 20 May 2010 15:28:20 +0000 (15:28 +0000)]
cluster.split command
westcott [Thu, 20 May 2010 15:19:57 +0000 (15:19 +0000)]
fixed phylip convert for cluster.split command
westcott [Thu, 20 May 2010 15:00:33 +0000 (15:00 +0000)]
added cluster.split command
westcott [Tue, 18 May 2010 12:31:11 +0000 (12:31 +0000)]
added split.abund comand
westcott [Mon, 17 May 2010 14:01:43 +0000 (14:01 +0000)]
change to phylo.diversity to make output = total branch length seen so far for each group instead of total branch length seen so far for each group / total branch length for that group
westcott [Fri, 14 May 2010 18:50:27 +0000 (18:50 +0000)]
1.10.0
westcott [Wed, 12 May 2010 12:15:09 +0000 (12:15 +0000)]
modified freq parameter be a percentage of numSeqs, added catchall command - not working right yet.
westcott [Tue, 11 May 2010 16:25:11 +0000 (16:25 +0000)]
added clearcut command
westcott [Mon, 10 May 2010 18:28:14 +0000 (18:28 +0000)]
added chop.seqs command
westcott [Mon, 10 May 2010 17:48:22 +0000 (17:48 +0000)]
fixed problem with class.fy.seqs where group totals did not add up. added constructors to sequence class to allow for just setting the unaligned field to save space.
westcott [Mon, 10 May 2010 16:59:29 +0000 (16:59 +0000)]
added make.group command
westcott [Mon, 10 May 2010 12:11:55 +0000 (12:11 +0000)]
worked on trim.seqs
westcott [Mon, 10 May 2010 12:11:55 +0000 (12:11 +0000)]
worked on trim.seqs
pschloss [Mon, 10 May 2010 11:10:37 +0000 (11:10 +0000)]
pds - modified strip barcode funcrtion in trimseqscommand
westcott [Fri, 7 May 2010 17:59:09 +0000 (17:59 +0000)]
changed confidence scores calculation in bayesian
westcott [Fri, 7 May 2010 16:45:56 +0000 (16:45 +0000)]
modified trim.seqs to account for primers of different lengths
westcott [Fri, 7 May 2010 15:00:59 +0000 (15:00 +0000)]
added diffs to trim.seqs
westcott [Fri, 7 May 2010 14:29:14 +0000 (14:29 +0000)]
working on trim.seqs
westcott [Fri, 7 May 2010 12:39:04 +0000 (12:39 +0000)]
changed groupfile in classify.seqs to reflect multiple fasta files
westcott [Wed, 5 May 2010 14:10:34 +0000 (14:10 +0000)]
filled out reference taxonomy with "unclassified" so that if a cutoff is used the summary file still adds up
westcott [Tue, 4 May 2010 15:05:05 +0000 (15:05 +0000)]
enabled ~
westcott [Tue, 4 May 2010 13:45:52 +0000 (13:45 +0000)]
fixed bug that caused bayesian cutoff not to work if iters > 100. fixed bug in trim.seqs caused by sequence length for qfile coming from fasta file.
westcott [Tue, 4 May 2010 12:41:07 +0000 (12:41 +0000)]
added phylo.diversity command. added hard parameter to cluster, hcluster and read.dist. modified remove.seqs so it can do multiple files at once.
westcott [Fri, 30 Apr 2010 13:50:47 +0000 (13:50 +0000)]
made get.oturep more memory efficient by breaking the work into 2 pieces.
westcott [Fri, 30 Apr 2010 12:01:35 +0000 (12:01 +0000)]
paralellized trim.seqs
westcott [Thu, 29 Apr 2010 13:54:23 +0000 (13:54 +0000)]
paralellized summary.seqs and added mpi code to it.
westcott [Thu, 29 Apr 2010 11:15:33 +0000 (11:15 +0000)]
paralellized screen.seqs and added mpi code to it. fixed bug with all mpi commands that was caused by the startindex line coming after the numSeqsPerProcess line, only occurred in files where the number of seqs could not be divide evenly between processes.
westcott [Wed, 28 Apr 2010 11:09:48 +0000 (11:09 +0000)]
added set.logfile command
westcott [Tue, 27 Apr 2010 18:53:09 +0000 (18:53 +0000)]
added name parameter to phylotype command
westcott [Tue, 27 Apr 2010 17:54:59 +0000 (17:54 +0000)]
reworked the classifiers summary file added groupfile option to classify.seqs, added mpi code to classifiers modification
westcott [Mon, 26 Apr 2010 15:05:21 +0000 (15:05 +0000)]
made classifier faster
westcott [Tue, 20 Apr 2010 12:50:01 +0000 (12:50 +0000)]
a few modifications for 1.9
westcott [Tue, 20 Apr 2010 11:34:53 +0000 (11:34 +0000)]
a few modifications for 1.9
westcott [Sat, 17 Apr 2010 00:10:32 +0000 (00:10 +0000)]
1.9
westcott [Fri, 16 Apr 2010 14:55:17 +0000 (14:55 +0000)]
1.9
pschloss [Wed, 14 Apr 2010 12:44:12 +0000 (12:44 +0000)]
pat's minor edits to distance calculations
westcott [Wed, 14 Apr 2010 11:32:59 +0000 (11:32 +0000)]
some changes while testing 1.9
westcott [Wed, 7 Apr 2010 12:55:09 +0000 (12:55 +0000)]
added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff, paralellized filter.seqs and bellerophon.
westcott [Wed, 17 Mar 2010 17:47:33 +0000 (17:47 +0000)]
finished mpi for filter.seqs
westcott [Wed, 17 Mar 2010 14:59:45 +0000 (14:59 +0000)]
testing
westcott [Tue, 16 Mar 2010 13:09:20 +0000 (13:09 +0000)]
modified mpi code to save ram by writing out every 10 seqs.
westcott [Fri, 12 Mar 2010 17:39:18 +0000 (17:39 +0000)]
added MPI to dist.seqs command
westcott [Thu, 11 Mar 2010 13:20:55 +0000 (13:20 +0000)]
testing mpi
westcott [Thu, 4 Mar 2010 18:35:56 +0000 (18:35 +0000)]
mothur with external build
westcott [Thu, 4 Mar 2010 14:50:33 +0000 (14:50 +0000)]
changes to filter.seqs
westcott [Wed, 3 Mar 2010 12:33:53 +0000 (12:33 +0000)]
added checks for ^C to quit command instead of program
westcott [Mon, 1 Mar 2010 11:59:21 +0000 (11:59 +0000)]
adding mothurout.h and .cpp to repo
westcott [Fri, 26 Feb 2010 15:08:15 +0000 (15:08 +0000)]
filter.seqs can now accept multiple fasta files
westcott [Fri, 26 Feb 2010 14:35:09 +0000 (14:35 +0000)]
created mothurOut class to handle logfiles
westcott [Thu, 25 Feb 2010 12:05:21 +0000 (12:05 +0000)]
added parse.list command
westcott [Wed, 24 Feb 2010 11:07:33 +0000 (11:07 +0000)]
finished chimera changes
westcott [Tue, 23 Feb 2010 19:41:26 +0000 (19:41 +0000)]
added warning about merging with something above cutoff to cluster. working on chimeras
westcott [Tue, 23 Feb 2010 19:31:30 +0000 (19:31 +0000)]
added warning about merging with something above cutoff to cluster. working on chimeras
westcott [Mon, 22 Feb 2010 17:22:22 +0000 (17:22 +0000)]
chimeras, fix to sabundvector and sharedsabundvector that caused getRabundVector to step out of bounds
westcott [Wed, 17 Feb 2010 13:30:52 +0000 (13:30 +0000)]
chimeras
westcott [Tue, 16 Feb 2010 15:23:05 +0000 (15:23 +0000)]
chimeracode
westcott [Fri, 12 Feb 2010 19:50:54 +0000 (19:50 +0000)]
working on chimeras
pschloss [Thu, 4 Feb 2010 21:06:01 +0000 (21:06 +0000)]
test
pschloss [Thu, 4 Feb 2010 15:57:46 +0000 (15:57 +0000)]
pat's ../ bug fix - test
pschloss [Thu, 4 Feb 2010 15:14:07 +0000 (15:14 +0000)]
pat's ../ bug fix
westcott [Wed, 3 Feb 2010 12:26:44 +0000 (12:26 +0000)]
added name option to read.tree for use in unifrac and parimony commands
pschloss [Tue, 2 Feb 2010 15:00:23 +0000 (15:00 +0000)]
pat's differences before v.1.8
westcott [Tue, 2 Feb 2010 14:33:49 +0000 (14:33 +0000)]
fixed bugs for 1.8
westcott [Thu, 28 Jan 2010 18:11:16 +0000 (18:11 +0000)]
fixed some bugs found while testing 1.8
westcott [Wed, 27 Jan 2010 21:08:49 +0000 (21:08 +0000)]
fixed some bugs found while testing 1.8
westcott [Wed, 27 Jan 2010 16:04:47 +0000 (16:04 +0000)]
added distance search method to classify.seqs