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git.donarmstrong.com Git - mothur.git/log
westcott [Mon, 18 Oct 2010 13:59:50 +0000 (13:59 +0000)]
added ifdefs for extern c
westcott [Mon, 18 Oct 2010 12:14:32 +0000 (12:14 +0000)]
testing metastats compile
westcott [Fri, 15 Oct 2010 16:46:19 +0000 (16:46 +0000)]
added pipeline commands which involved change to command factory and command class. fixed bug in unifrac.unwieghted
westcott [Tue, 5 Oct 2010 10:08:43 +0000 (10:08 +0000)]
paralellized phylo.diversity
westcott [Mon, 4 Oct 2010 18:03:32 +0000 (18:03 +0000)]
paralellized rarefaction.single
westcott [Mon, 4 Oct 2010 09:55:59 +0000 (09:55 +0000)]
changed name of parse.fastaq command to fastq.info
westcott [Thu, 30 Sep 2010 10:51:56 +0000 (10:51 +0000)]
added parse.fastaq command, added permute option to venn command, fixed bug with output redirect in chimera commands
westcott [Tue, 28 Sep 2010 16:31:21 +0000 (16:31 +0000)]
added distance option to summary.shared
westcott [Fri, 24 Sep 2010 14:03:47 +0000 (14:03 +0000)]
added get.lineage and remove.lineage commands
westcott [Thu, 23 Sep 2010 17:53:42 +0000 (17:53 +0000)]
fixed order of unifrac commands so that it matches the summary commands
westcott [Thu, 23 Sep 2010 15:31:47 +0000 (15:31 +0000)]
added cluster.fragments command as well as the nseqs parameter to the venn command
westcott [Tue, 21 Sep 2010 14:55:28 +0000 (14:55 +0000)]
added mothur executable to cvs
westcott [Tue, 21 Sep 2010 10:53:52 +0000 (10:53 +0000)]
added split.groups command
westcott [Mon, 20 Sep 2010 16:10:59 +0000 (16:10 +0000)]
changed how we name the make.group groups file, and filter file in filter.seqs, finished working on metastats.
westcott [Fri, 17 Sep 2010 17:06:42 +0000 (17:06 +0000)]
bug fixes
westcott [Fri, 17 Sep 2010 16:55:59 +0000 (16:55 +0000)]
bug fixes
westcott [Fri, 17 Sep 2010 12:36:19 +0000 (12:36 +0000)]
working on megastats
westcott [Thu, 16 Sep 2010 10:34:29 +0000 (10:34 +0000)]
initial add of metastats
westcott [Wed, 15 Sep 2010 11:49:02 +0000 (11:49 +0000)]
added normalize.shared command
westcott [Wed, 15 Sep 2010 11:24:31 +0000 (11:24 +0000)]
added normalize.shared command
westcott [Wed, 15 Sep 2010 09:51:33 +0000 (09:51 +0000)]
paralellized summary.shared
westcott [Thu, 9 Sep 2010 15:10:01 +0000 (15:10 +0000)]
done testing 1.13.0
westcott [Wed, 8 Sep 2010 15:36:06 +0000 (15:36 +0000)]
testing 1.13.0
westcott [Sat, 4 Sep 2010 00:24:30 +0000 (00:24 +0000)]
working on testing for 1.13
westcott [Fri, 3 Sep 2010 10:34:35 +0000 (10:34 +0000)]
working on testing
westcott [Wed, 1 Sep 2010 16:57:44 +0000 (16:57 +0000)]
unifrac parallelization done, changed dist.seqs output=square to calc all distance twice instead of converting the matrix.
westcott [Wed, 1 Sep 2010 13:05:31 +0000 (13:05 +0000)]
working on unifrac parallelization
westcott [Tue, 31 Aug 2010 17:55:38 +0000 (17:55 +0000)]
working on parallelizing unifrac.unweighted.
westcott [Tue, 31 Aug 2010 16:03:14 +0000 (16:03 +0000)]
working on parallelizing unifrac.weighted.
westcott [Mon, 30 Aug 2010 15:14:18 +0000 (15:14 +0000)]
sped up unifrac unweighted.
westcott [Mon, 30 Aug 2010 13:49:18 +0000 (13:49 +0000)]
sped up unifrac weighted.
westcott [Fri, 27 Aug 2010 15:21:38 +0000 (15:21 +0000)]
made read.tree not require a groupfile, if one is not given all seqs are assumed to be from one group
westcott [Fri, 27 Aug 2010 14:18:38 +0000 (14:18 +0000)]
fixed phylo.diversity
westcott [Fri, 27 Aug 2010 13:50:03 +0000 (13:50 +0000)]
fixed phylo.diversity
pschloss [Thu, 26 Aug 2010 20:48:56 +0000 (20:48 +0000)]
changes to read.tree
pschloss [Thu, 26 Aug 2010 20:15:27 +0000 (20:15 +0000)]
modified splitAtComma in mothurout command
westcott [Thu, 26 Aug 2010 15:18:14 +0000 (15:18 +0000)]
added clearcut source to mothur, fixed mislabeled sharedcalcs
westcott [Thu, 26 Aug 2010 15:18:13 +0000 (15:18 +0000)]
added clearcut source to mothur, fixed mislabeled sharedcalcs
pschloss [Thu, 26 Aug 2010 13:04:35 +0000 (13:04 +0000)]
changes to read.otu(list/shared) - took out substr calls
pschloss [Thu, 26 Aug 2010 11:42:23 +0000 (11:42 +0000)]
took out debugging output code from distance calculators
westcott [Tue, 24 Aug 2010 17:58:20 +0000 (17:58 +0000)]
added sharedRabundFloatVector class to represent the relabund file. modified read.otu command, readotu class, and input class to read it. added relabund type to heatmap.bin command.
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