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git.donarmstrong.com Git - mothur.git/log
westcott [Tue, 24 Aug 2010 11:51:33 +0000 (11:51 +0000)]
moved utilities out of mothur.h and into mothurOut class.
westcott [Mon, 23 Aug 2010 16:11:13 +0000 (16:11 +0000)]
filter.seqs bug change
westcott [Mon, 23 Aug 2010 12:32:48 +0000 (12:32 +0000)]
numSeqs passing fix
pschloss [Mon, 23 Aug 2010 11:52:06 +0000 (11:52 +0000)]
added a few evenness calculators and fixed a couple of bugs in filter.seqs and pre.cluster
pschloss [Fri, 20 Aug 2010 19:25:59 +0000 (19:25 +0000)]
fixed filterseqscommand bug where trump wasn't being used
westcott [Fri, 20 Aug 2010 17:45:36 +0000 (17:45 +0000)]
pre.cluster
westcott [Fri, 20 Aug 2010 17:17:35 +0000 (17:17 +0000)]
pre.cluster
westcott [Fri, 20 Aug 2010 14:58:44 +0000 (14:58 +0000)]
modified precluster to use less memory.
westcott [Fri, 20 Aug 2010 12:40:46 +0000 (12:40 +0000)]
changed file divide for trim.seqs
westcott [Thu, 19 Aug 2010 16:28:18 +0000 (16:28 +0000)]
changed how we break up the files on parallelized commands to avoid scanning file.
westcott [Thu, 19 Aug 2010 10:41:32 +0000 (10:41 +0000)]
modified calculators to use doubles, added numotu and fontsize parameters to heatmap as well as adding more sorting options. fixed bug in mothur.h setfilepositions that caused accession names to be truncated when windows line endings were used.
pschloss [Thu, 12 Aug 2010 14:53:23 +0000 (14:53 +0000)]
fixed a trimming bug in sffinfo which occurs when the right trim point is smaller than the left trim point
pschloss [Thu, 12 Aug 2010 13:04:22 +0000 (13:04 +0000)]
fixed int bug in simpson.cpp
westcott [Fri, 6 Aug 2010 19:40:11 +0000 (19:40 +0000)]
added oldfasta and column parameter to dist.seqs so you can append distances to an existing distance file.
westcott [Fri, 6 Aug 2010 13:36:36 +0000 (13:36 +0000)]
added versioning info to all shortcut files mothur makes.
westcott [Thu, 5 Aug 2010 14:51:45 +0000 (14:51 +0000)]
added summary, collect, and scale parameters to phylo.diversity command.
westcott [Thu, 5 Aug 2010 10:52:19 +0000 (10:52 +0000)]
fixed bug with creation of .tree.sum file
westcott [Tue, 3 Aug 2010 17:35:54 +0000 (17:35 +0000)]
added countgaps parameter to chop.seqs command
westcott [Tue, 3 Aug 2010 16:16:46 +0000 (16:16 +0000)]
modified the engine to extract the path of mothur executable if argv does not contain it. added default setting to set.dir to change directories to where mothur.exe is located. added splitAtChar to mothur.h which splits a string by the character passed in.
westcott [Mon, 2 Aug 2010 18:05:57 +0000 (18:05 +0000)]
fixed bug with phylo.diversity. not calculating as intended.
westcott [Fri, 30 Jul 2010 16:53:56 +0000 (16:53 +0000)]
changes for 1.12.2
westcott [Fri, 30 Jul 2010 12:55:01 +0000 (12:55 +0000)]
changes for 1.12.2
pschloss [Thu, 29 Jul 2010 20:50:30 +0000 (20:50 +0000)]
another attempt to fix sffinfo
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
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