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git.donarmstrong.com Git - mothur.git/log
westcott [Tue, 19 Jul 2011 16:09:58 +0000 (16:09 +0000)]
added blastlocation to chimera.slayer and fixed issue with clearcut getting current file
westcott [Tue, 19 Jul 2011 13:53:57 +0000 (13:53 +0000)]
added shared file type to get.groups and remove.groups
westcott [Mon, 18 Jul 2011 18:27:18 +0000 (18:27 +0000)]
changed normalize.shared and sub.sample commands to fix bug in normalize.shared and make otu labels persist.
westcott [Fri, 15 Jul 2011 19:50:30 +0000 (19:50 +0000)]
rewrote metastats command in c++, added mothurRemove function to handle ~ error. fixed bug with classify.otu summary file. added check for isnum in quality scores read.
westcott [Wed, 6 Jul 2011 14:43:57 +0000 (14:43 +0000)]
added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error commands. added clear.memory command. added error message to chimera.slayer and chimera.uchime to avoid user entering both a namefile and reference file.
pschloss [Tue, 5 Jul 2011 17:52:54 +0000 (17:52 +0000)]
minor mods to seq.error
westcott [Wed, 29 Jun 2011 11:25:17 +0000 (11:25 +0000)]
paralellized the indicator command
westcott [Tue, 28 Jun 2011 15:11:36 +0000 (15:11 +0000)]
small bug with trimming of quality scores over a window. lost last base if sequence was good over entire length.
westcott [Tue, 28 Jun 2011 11:57:50 +0000 (11:57 +0000)]
indicator command
pschloss [Tue, 28 Jun 2011 11:48:28 +0000 (11:48 +0000)]
changed citation for uchime
westcott [Tue, 28 Jun 2011 10:20:10 +0000 (10:20 +0000)]
indicator command
westcott [Tue, 21 Jun 2011 16:07:40 +0000 (16:07 +0000)]
added cutoff change to mgcluster
westcott [Tue, 21 Jun 2011 16:04:01 +0000 (16:04 +0000)]
added cutoff change to hcluster
westcott [Tue, 21 Jun 2011 11:25:46 +0000 (11:25 +0000)]
descriptions
westcott [Mon, 20 Jun 2011 16:37:41 +0000 (16:37 +0000)]
added command descriptions
westcott [Fri, 17 Jun 2011 14:36:52 +0000 (14:36 +0000)]
1.20.0
pschloss [Tue, 14 Jun 2011 17:51:02 +0000 (17:51 +0000)]
small change to shhh.seqs
westcott [Tue, 14 Jun 2011 16:53:32 +0000 (16:53 +0000)]
working on current change
westcott [Tue, 14 Jun 2011 14:22:10 +0000 (14:22 +0000)]
working on current change
pschloss [Mon, 13 Jun 2011 14:23:44 +0000 (14:23 +0000)]
removed some testing changes i made to classify.seqs
pschloss [Thu, 9 Jun 2011 19:47:48 +0000 (19:47 +0000)]
trim.flows mod
pschloss [Thu, 9 Jun 2011 15:21:36 +0000 (15:21 +0000)]
some of pat's small modifications
westcott [Fri, 3 Jun 2011 19:41:36 +0000 (19:41 +0000)]
fixed bug with blastdb.cpp
westcott [Fri, 3 Jun 2011 17:17:33 +0000 (17:17 +0000)]
fixed bug with blastdb.cpp
westcott [Wed, 1 Jun 2011 17:37:36 +0000 (17:37 +0000)]
added headers to shared and relabund files
westcott [Wed, 1 Jun 2011 14:36:06 +0000 (14:36 +0000)]
added count.seqs command and made some modifcations to the uchime code to allow it to build properly in cygwin
westcott [Wed, 1 Jun 2011 14:36:06 +0000 (14:36 +0000)]
added count.seqs command and made some modifcations to the uchime code to allow it to build properly in cygwin
westcott [Tue, 31 May 2011 15:36:25 +0000 (15:36 +0000)]
working on removing pointers from chimera.slayer to eliminate pesky memory leaks
pschloss [Tue, 31 May 2011 12:23:23 +0000 (12:23 +0000)]
changes to beta diversity calculators
westcott [Fri, 27 May 2011 18:19:15 +0000 (18:19 +0000)]
finished consensus.seqs cutoff change
westcott [Fri, 27 May 2011 17:59:12 +0000 (17:59 +0000)]
added deunique.tree command
westcott [Fri, 27 May 2011 15:37:04 +0000 (15:37 +0000)]
captured stdout from system command, fixed bug in trim.seqs added error checks for blast exes to blastdb.cpp
westcott [Thu, 26 May 2011 14:20:36 +0000 (14:20 +0000)]
v 19.3
westcott [Tue, 24 May 2011 19:39:22 +0000 (19:39 +0000)]
paralellized seq.error and dist.shared added some error checks to libshuff and dist.seqs
westcott [Tue, 24 May 2011 19:39:22 +0000 (19:39 +0000)]
paralellized seq.error and dist.shared added some error checks to libshuff and dist.seqs
westcott [Fri, 20 May 2011 14:08:08 +0000 (14:08 +0000)]
added path search for lookup file in shhh.seqs
pschloss [Fri, 20 May 2011 13:52:43 +0000 (13:52 +0000)]
add lookup files for shhh.seqs
westcott [Fri, 20 May 2011 13:30:51 +0000 (13:30 +0000)]
changed blastdb.cpp to no include sequence names in blast input filenames. modified phylo.diversity to allow for no group file.
westcott [Fri, 20 May 2011 10:48:01 +0000 (10:48 +0000)]
finished adding the names option to trim.seqs
pschloss [Wed, 18 May 2011 21:02:07 +0000 (21:02 +0000)]
mods to shhh.seqs and trim.flows to fix eye candy output
westcott [Wed, 18 May 2011 15:15:43 +0000 (15:15 +0000)]
added name option to trim.seqs
westcott [Wed, 18 May 2011 14:44:12 +0000 (14:44 +0000)]
fixed bug with trim.seqs allfiles=t
westcott [Wed, 18 May 2011 13:22:43 +0000 (13:22 +0000)]
fixed bug with trim.seqs allfiles=t
westcott [Wed, 18 May 2011 12:32:06 +0000 (12:32 +0000)]
fixed bug in chimera.uchime
westcott [Tue, 17 May 2011 19:06:36 +0000 (19:06 +0000)]
added parameter to chimera.uchime
westcott [Mon, 16 May 2011 19:35:33 +0000 (19:35 +0000)]
added chimera.uchime
westcott [Mon, 16 May 2011 19:22:44 +0000 (19:22 +0000)]
added chimera.uchime
westcott [Mon, 16 May 2011 19:22:44 +0000 (19:22 +0000)]
added chimera.uchime
westcott [Wed, 11 May 2011 14:52:39 +0000 (14:52 +0000)]
working on citations
westcott [Tue, 10 May 2011 16:55:03 +0000 (16:55 +0000)]
added citation function to commands
westcott [Tue, 10 May 2011 16:44:40 +0000 (16:44 +0000)]
added citation function to commands
westcott [Mon, 9 May 2011 15:52:45 +0000 (15:52 +0000)]
1.19.0
westcott [Mon, 9 May 2011 11:54:45 +0000 (11:54 +0000)]
1.19.0
pschloss [Sun, 8 May 2011 02:36:30 +0000 (02:36 +0000)]
more chimera.slayer debugging
pschloss [Fri, 6 May 2011 18:04:50 +0000 (18:04 +0000)]
added kmer stuff
pschloss [Fri, 6 May 2011 17:47:04 +0000 (17:47 +0000)]
more chimera.slayer stuff
pschloss [Fri, 6 May 2011 16:14:31 +0000 (16:14 +0000)]
working on search=dist in chimera.slayer
pschloss [Fri, 6 May 2011 14:53:54 +0000 (14:53 +0000)]
working on search=dist in chimera.slayer
westcott [Fri, 6 May 2011 12:32:49 +0000 (12:32 +0000)]
fixed template=self thing
pschloss [Fri, 6 May 2011 00:41:14 +0000 (00:41 +0000)]
chimera.slayer debugging
pschloss [Thu, 5 May 2011 21:45:48 +0000 (21:45 +0000)]
chimera.slayer debugging
pschloss [Thu, 5 May 2011 20:42:45 +0000 (20:42 +0000)]
chimera.slayer debugging
pschloss [Thu, 5 May 2011 14:59:11 +0000 (14:59 +0000)]
changed tags on temp blast db to include template name
pschloss [Thu, 5 May 2011 14:26:37 +0000 (14:26 +0000)]
changed tags on temp blast db to include template name
westcott [Wed, 4 May 2011 20:37:19 +0000 (20:37 +0000)]
trim.seqs fix of gobble
westcott [Wed, 4 May 2011 20:18:12 +0000 (20:18 +0000)]
chimera.slayer
westcott [Wed, 4 May 2011 20:07:48 +0000 (20:07 +0000)]
chimera.slayer
westcott [Wed, 4 May 2011 15:36:44 +0000 (15:36 +0000)]
changes for chimera slayer using last column
westcott [Wed, 4 May 2011 15:25:08 +0000 (15:25 +0000)]
changes for chimera slayer
westcott [Wed, 4 May 2011 14:34:28 +0000 (14:34 +0000)]
changes for chimera slayer
westcott [Wed, 4 May 2011 14:11:02 +0000 (14:11 +0000)]
changes for chimera slayer
pschloss [Tue, 3 May 2011 18:48:05 +0000 (18:48 +0000)]
incorporation of nast-ier code / removed a cout
pschloss [Tue, 3 May 2011 18:43:48 +0000 (18:43 +0000)]
incorporation of nast-ier code
westcott [Tue, 3 May 2011 17:06:49 +0000 (17:06 +0000)]
maligner change
westcott [Tue, 3 May 2011 16:29:07 +0000 (16:29 +0000)]
fixed id match
westcott [Tue, 3 May 2011 13:28:30 +0000 (13:28 +0000)]
sped up realign
westcott [Tue, 3 May 2011 13:20:50 +0000 (13:20 +0000)]
changed defaults in slayer to minsnp=10 and realign=t
westcott [Tue, 3 May 2011 13:15:50 +0000 (13:15 +0000)]
fixed bug with realigner for chimera slayer
westcott [Tue, 3 May 2011 13:15:50 +0000 (13:15 +0000)]
fixed bug with realigner for chimera slayer
westcott [Mon, 2 May 2011 16:38:34 +0000 (16:38 +0000)]
modified chimera.slayer bootstrap to bump up to 1000 on borderline bootstrap values
westcott [Mon, 2 May 2011 16:31:36 +0000 (16:31 +0000)]
modified chimera.slayer bootstrap to bump up to 1000 on borderline bootstrap values
westcott [Mon, 2 May 2011 16:27:28 +0000 (16:27 +0000)]
modified chimera.slayer bootstrap to bump up to 1000 on borderline bootstrap values
westcott [Fri, 29 Apr 2011 20:00:06 +0000 (20:00 +0000)]
working on chimera.slayer
westcott [Fri, 29 Apr 2011 18:14:49 +0000 (18:14 +0000)]
working on chimera.slayer
westcott [Wed, 27 Apr 2011 19:37:40 +0000 (19:37 +0000)]
working on slayer bug
pschloss [Wed, 27 Apr 2011 10:22:58 +0000 (10:22 +0000)]
tracking down chimera.slayer issue
westcott [Tue, 26 Apr 2011 19:44:22 +0000 (19:44 +0000)]
added current as option is lists of file names, processors now outputted with current options added flow type to current files, added queryName != templateName in decalc.findclosest for slayer
westcott [Tue, 26 Apr 2011 11:45:58 +0000 (11:45 +0000)]
blast queryName=templateSeq name bug
westcott [Tue, 26 Apr 2011 11:40:11 +0000 (11:40 +0000)]
*** empty log message ***
westcott [Mon, 25 Apr 2011 18:00:39 +0000 (18:00 +0000)]
minor bug in chimera maligner
westcott [Mon, 25 Apr 2011 11:31:20 +0000 (11:31 +0000)]
fixed ties issue in maligner getBlastSeqs
pschloss [Thu, 21 Apr 2011 20:08:54 +0000 (20:08 +0000)]
small things with chimera.slayer
pschloss [Wed, 20 Apr 2011 16:54:49 +0000 (16:54 +0000)]
some alterations to chimera.slayer
westcott [Tue, 19 Apr 2011 10:08:17 +0000 (10:08 +0000)]
finished chimera.slayer template=self change
westcott [Mon, 18 Apr 2011 17:55:59 +0000 (17:55 +0000)]
modified chimera.slayer template=self
pschloss [Mon, 18 Apr 2011 17:25:11 +0000 (17:25 +0000)]
small fix to refchimeratest.cpp
pschloss [Mon, 18 Apr 2011 15:01:44 +0000 (15:01 +0000)]
tie breaker fix to chimera.slayer
pschloss [Mon, 18 Apr 2011 14:08:31 +0000 (14:08 +0000)]
tie breaker fix to chimera.slayer
westcott [Fri, 15 Apr 2011 15:25:08 +0000 (15:25 +0000)]
1.18.1
westcott [Mon, 11 Apr 2011 19:32:07 +0000 (19:32 +0000)]
1.18.0 - fixed make.shared abort issue
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