]>
git.donarmstrong.com Git - mothur.git/log
westcott [Thu, 29 Jul 2010 13:09:06 +0000 (13:09 +0000)]
1.12.1
pschloss [Thu, 29 Jul 2010 06:06:22 +0000 (06:06 +0000)]
another pds fix to sffinfo
pschloss [Thu, 29 Jul 2010 06:05:49 +0000 (06:05 +0000)]
another pds fix to sffinfo
pschloss [Thu, 29 Jul 2010 04:01:58 +0000 (04:01 +0000)]
pds' small change to sffinfo
westcott [Wed, 28 Jul 2010 15:09:56 +0000 (15:09 +0000)]
some bug fixes
pschloss [Wed, 28 Jul 2010 14:55:58 +0000 (14:55 +0000)]
pat's slight modifications to trim.seqs
westcott [Fri, 23 Jul 2010 14:27:45 +0000 (14:27 +0000)]
1.12.0
westcott [Thu, 22 Jul 2010 18:52:22 +0000 (18:52 +0000)]
fixes while testing 1.12.0
westcott [Tue, 20 Jul 2010 14:40:07 +0000 (14:40 +0000)]
added tempdefault to set.dir and fixed bug with padding type in sffinfo.
westcott [Mon, 19 Jul 2010 16:20:25 +0000 (16:20 +0000)]
added ordergroup parameter to read.otu
pschloss [Mon, 19 Jul 2010 14:57:36 +0000 (14:57 +0000)]
pat's updates on 7/19/10
westcott [Mon, 19 Jul 2010 14:39:18 +0000 (14:39 +0000)]
added compile time default path
westcott [Mon, 19 Jul 2010 10:50:54 +0000 (10:50 +0000)]
added fasta, qfile, trim, accnos and sfftxt parameter to sffinfo command. added lci hci outputs for thetayc
westcott [Thu, 15 Jul 2010 20:33:00 +0000 (20:33 +0000)]
sffinfo command is working
westcott [Thu, 15 Jul 2010 19:52:35 +0000 (19:52 +0000)]
sffinfo command is working
westcott [Thu, 15 Jul 2010 12:21:55 +0000 (12:21 +0000)]
working on sffinfo
westcott [Wed, 14 Jul 2010 16:52:56 +0000 (16:52 +0000)]
working on sffinfo command.
westcott [Wed, 14 Jul 2010 16:12:53 +0000 (16:12 +0000)]
working on sffinfo command.
westcott [Wed, 14 Jul 2010 16:03:07 +0000 (16:03 +0000)]
working on sffinfo command.
pschloss [Wed, 14 Jul 2010 12:14:53 +0000 (12:14 +0000)]
pat's changes to trim.seqs
westcott [Wed, 14 Jul 2010 11:45:40 +0000 (11:45 +0000)]
started work on sffinfo command. fixed bug across all paralellized commands if the file position was too big to fit in an int.
pschloss [Wed, 7 Jul 2010 19:36:36 +0000 (19:36 +0000)]
modified makefile and sensspeccommand files
pschloss [Tue, 6 Jul 2010 20:30:15 +0000 (20:30 +0000)]
sens.spec changes
westcott [Tue, 6 Jul 2010 15:51:21 +0000 (15:51 +0000)]
fixed trim.seqs bug
westcott [Tue, 6 Jul 2010 13:31:58 +0000 (13:31 +0000)]
rechecking in
westcott [Tue, 6 Jul 2010 13:30:30 +0000 (13:30 +0000)]
trim.seqs couts
westcott [Wed, 30 Jun 2010 16:56:43 +0000 (16:56 +0000)]
modified trim.seqs to split by primer name if primer name is given, and warn if duplicate barcodes are used. made get.sharedseqs compatible with other fasta formatted software, started adding memory checks to error reporter in mothurout.cpp
westcott [Mon, 28 Jun 2010 18:32:11 +0000 (18:32 +0000)]
added groups option to get.oturep command
westcott [Thu, 24 Jun 2010 17:18:38 +0000 (17:18 +0000)]
created blank accnos in chimera commands if no seqs are deemed chimeric. modified get.seqs and remove.seqs to handle blank files
westcott [Wed, 23 Jun 2010 19:41:53 +0000 (19:41 +0000)]
fixed bug with cluster class. when we added the change for average neighbor to update the cutoff, we did not also pass the cutoff to single linkage. so because of inheritance cluster its instead of the update in singlelinkage.
westcott [Wed, 23 Jun 2010 17:42:48 +0000 (17:42 +0000)]
fixed cluster.split with average method
westcott [Tue, 22 Jun 2010 17:32:48 +0000 (17:32 +0000)]
finished get.relabund command
westcott [Tue, 22 Jun 2010 17:32:48 +0000 (17:32 +0000)]
finished get.relabund command
westcott [Tue, 22 Jun 2010 12:40:41 +0000 (12:40 +0000)]
added mpi code to cluster.split command
westcott [Tue, 22 Jun 2010 11:41:29 +0000 (11:41 +0000)]
added mpi code to cluster.split command
westcott [Mon, 21 Jun 2010 16:58:45 +0000 (16:58 +0000)]
added degap.seqs command
westcott [Mon, 21 Jun 2010 16:08:42 +0000 (16:08 +0000)]
modified chimera commands to process multiple fasta files and added checks to pintail to look for consfile and quantile files to save time.
westcott [Fri, 18 Jun 2010 18:47:51 +0000 (18:47 +0000)]
removed blast files generated by chimera.slayer, altered makefile to allow for 64bit builds
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