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git.donarmstrong.com Git - mothur.git/log
westcott [Wed, 5 Jan 2011 13:07:39 +0000 (13:07 +0000)]
removed various build warnings
westcott [Wed, 5 Jan 2011 11:37:25 +0000 (11:37 +0000)]
added metadata file as input to corr.axes
westcott [Tue, 4 Jan 2011 18:41:51 +0000 (18:41 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 18:41:42 +0000 (18:41 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 18:35:45 +0000 (18:35 +0000)]
Changed back to xcode build.
westcott [Tue, 4 Jan 2011 15:40:55 +0000 (15:40 +0000)]
removed parse.sff command and made its functionality part of sffinfo command. fixed issues with corr.axes method=kendall.
pschloss [Tue, 4 Jan 2011 11:54:21 +0000 (11:54 +0000)]
modifications to shhh.seqs
westcott [Mon, 3 Jan 2011 19:16:52 +0000 (19:16 +0000)]
added template=self capability to chimers.slayer, worked on corr.axes and added accnos compare function to get.seqs
pschloss [Fri, 31 Dec 2010 16:42:32 +0000 (16:42 +0000)]
added shhh.seqs command
pschloss [Fri, 31 Dec 2010 16:35:11 +0000 (16:35 +0000)]
added shhh.seqs command
pschloss [Thu, 23 Dec 2010 21:37:11 +0000 (21:37 +0000)]
addition of trim.flows
westcott [Thu, 23 Dec 2010 19:41:30 +0000 (19:41 +0000)]
fixed memory leak in maligner minCoverageFilter function used by chimera slayer
westcott [Thu, 23 Dec 2010 19:05:17 +0000 (19:05 +0000)]
fixed memory leak in decalc findClosest function used by chimera slayer
westcott [Wed, 22 Dec 2010 19:03:19 +0000 (19:03 +0000)]
chimera.slayer fix
westcott [Wed, 22 Dec 2010 14:58:11 +0000 (14:58 +0000)]
fixed trim.seqs weird characters thing
westcott [Wed, 22 Dec 2010 13:22:04 +0000 (13:22 +0000)]
added output filenames and m->control_pressed stuff to seq.error command
pschloss [Tue, 21 Dec 2010 20:35:44 +0000 (20:35 +0000)]
more changes to error.seqs command and quality scores classses
pschloss [Mon, 20 Dec 2010 12:29:36 +0000 (12:29 +0000)]
pat's changes to seq.error command
westcott [Fri, 17 Dec 2010 18:54:42 +0000 (18:54 +0000)]
added design parameter to the indicator command
westcott [Fri, 17 Dec 2010 16:46:03 +0000 (16:46 +0000)]
added odum, canberra, structchi2, structchord, structeuclidean, gower, hellinger, structkulczynski, manhattan, structpearson, soergel, spearman, speciesprofile, memchi2, memchord, memeuclidean, hamming, mempearson calcs
westcott [Fri, 17 Dec 2010 13:47:10 +0000 (13:47 +0000)]
fixed bug with trim.seqs- when a file is blank for a grouping mothur removed it, but since multiple barcodes went to the same group the allfiles list had the same name more than once, so when it went to check if it was blank again it didn't exist
westcott [Tue, 14 Dec 2010 14:03:00 +0000 (14:03 +0000)]
added confidence scores to get.lineage and remove.lineage
westcott [Mon, 13 Dec 2010 20:33:34 +0000 (20:33 +0000)]
added summary file to classify.otu
westcott [Mon, 13 Dec 2010 13:55:30 +0000 (13:55 +0000)]
classify.seqs summary file fix
westcott [Fri, 10 Dec 2010 14:50:00 +0000 (14:50 +0000)]
rolled back metastats workspace change
westcott [Fri, 10 Dec 2010 12:58:53 +0000 (12:58 +0000)]
added shared file to catchall command
westcott [Wed, 8 Dec 2010 21:51:24 +0000 (21:51 +0000)]
metastats double* to double fix for windows
westcott [Wed, 8 Dec 2010 17:39:56 +0000 (17:39 +0000)]
consensus.seqs summary file change
westcott [Wed, 8 Dec 2010 16:52:46 +0000 (16:52 +0000)]
get.oturep ifstream
westcott [Wed, 8 Dec 2010 16:37:28 +0000 (16:37 +0000)]
get.oturep change and trim.seqs fix
westcott [Wed, 8 Dec 2010 15:51:45 +0000 (15:51 +0000)]
catchall windows fix
westcott [Tue, 7 Dec 2010 17:14:58 +0000 (17:14 +0000)]
consensus.seqs can now find a consensus on a whole fasta file without needing a listfile
pschloss [Tue, 7 Dec 2010 13:14:09 +0000 (13:14 +0000)]
changes to seqerrorcommand
westcott [Tue, 7 Dec 2010 13:03:17 +0000 (13:03 +0000)]
fixed indicator grouping problem
westcott [Mon, 6 Dec 2010 22:35:06 +0000 (22:35 +0000)]
modified trim.seqs to speed up the append with multiple processors
westcott [Mon, 6 Dec 2010 12:47:44 +0000 (12:47 +0000)]
added summary output to catchall command
westcott [Fri, 3 Dec 2010 19:53:27 +0000 (19:53 +0000)]
fixed indicator command bug
westcott [Fri, 3 Dec 2010 11:08:08 +0000 (11:08 +0000)]
fixed craig nelsons weighted bug and paralellized parsimony
westcott [Mon, 29 Nov 2010 14:21:39 +0000 (14:21 +0000)]
added consensus.seqs command
westcott [Mon, 22 Nov 2010 19:43:24 +0000 (19:43 +0000)]
finished wrapper for catchall
westcott [Mon, 22 Nov 2010 13:24:01 +0000 (13:24 +0000)]
added group option to trim.seqs so you can provide your own groupfile instead of using an oligos file to make one.
westcott [Fri, 19 Nov 2010 13:12:27 +0000 (13:12 +0000)]
added indicator command
westcott [Fri, 12 Nov 2010 12:43:09 +0000 (12:43 +0000)]
added get.otus and remove.otus commands
westcott [Wed, 10 Nov 2010 14:39:31 +0000 (14:39 +0000)]
added get.groups and remove.groups commands
westcott [Wed, 10 Nov 2010 11:37:18 +0000 (11:37 +0000)]
finished sub.sample command
westcott [Tue, 9 Nov 2010 17:40:05 +0000 (17:40 +0000)]
parsimony calculator changed order of groups to reflect change in shared Utils made to make output of summary.shared match unifrac commands
westcott [Mon, 8 Nov 2010 14:40:33 +0000 (14:40 +0000)]
changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes
westcott [Mon, 8 Nov 2010 13:55:38 +0000 (13:55 +0000)]
fixed cluster.split bug
westcott [Mon, 8 Nov 2010 11:58:26 +0000 (11:58 +0000)]
cluster.split fix
westcott [Fri, 5 Nov 2010 20:02:24 +0000 (20:02 +0000)]
fixed metastats, added resize to cluster.classic, added code to kill children if parent is unable to spawn and dies.
westcott [Fri, 5 Nov 2010 19:26:09 +0000 (19:26 +0000)]
cluster.split fix
westcott [Tue, 2 Nov 2010 16:30:16 +0000 (16:30 +0000)]
changed cluster.classic so that it does not adjust the cutoff
westcott [Tue, 2 Nov 2010 15:14:07 +0000 (15:14 +0000)]
fixed bug with normalize.shared, printed out numbins twice. fixed bug with summary.single caused if you had too many groups to open all files at once.
westcott [Tue, 2 Nov 2010 11:49:10 +0000 (11:49 +0000)]
fixed cluster.classic and added weighted method to hcluster
westcott [Fri, 29 Oct 2010 18:25:47 +0000 (18:25 +0000)]
added cluster.classic command
westcott [Fri, 29 Oct 2010 18:13:12 +0000 (18:13 +0000)]
added cluster.classic command
westcott [Wed, 27 Oct 2010 16:03:59 +0000 (16:03 +0000)]
fixed helps
westcott [Wed, 27 Oct 2010 15:55:49 +0000 (15:55 +0000)]
fixing helps
westcott [Tue, 26 Oct 2010 17:47:35 +0000 (17:47 +0000)]
done testing 1.14.0
westcott [Tue, 26 Oct 2010 16:36:02 +0000 (16:36 +0000)]
done testing 1.14.0
westcott [Tue, 26 Oct 2010 12:06:29 +0000 (12:06 +0000)]
fixes while testing
westcott [Mon, 25 Oct 2010 14:54:52 +0000 (14:54 +0000)]
added remove file option to pipeline command in user mode
westcott [Mon, 25 Oct 2010 13:59:04 +0000 (13:59 +0000)]
testing 1.14.0
westcott [Mon, 25 Oct 2010 13:42:22 +0000 (13:42 +0000)]
testing 1.14.0
westcott [Wed, 20 Oct 2010 18:16:33 +0000 (18:16 +0000)]
added pairwise.seqs
westcott [Tue, 19 Oct 2010 16:51:27 +0000 (16:51 +0000)]
fixed bug with aligner and longest base. added deunique.seqs command.
westcott [Tue, 19 Oct 2010 11:28:25 +0000 (11:28 +0000)]
fixed phylo.diversity and made trim.seqs with allfiles=T open one file at a time.
westcott [Mon, 18 Oct 2010 18:02:48 +0000 (18:02 +0000)]
fixed unifrac.weighted
westcott [Mon, 18 Oct 2010 16:14:10 +0000 (16:14 +0000)]
fixed unifrac.unweighted
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.
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