mothur.git
4 years agoupdate .gitignore master
Kathryn Iverson [Tue, 22 Apr 2014 13:08:22 +0000 (09:08 -0400)]
update .gitignore

4 years agopre.cluster unable to spawn necessary processes adjustment.
Sarah Westcott [Wed, 9 Apr 2014 13:18:00 +0000 (09:18 -0400)]
pre.cluster unable to spawn necessary processes adjustment.

4 years agoadded oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info...
Sarah Westcott [Wed, 9 Apr 2014 13:13:12 +0000 (09:13 -0400)]
added oligos class. added check orient parameter to trim.flows, sffinfo, fastq.info, and make.contigs.

4 years agoworking on sra and get.mimarkspackage commands. added file parameter to cluster...
Sarah Westcott [Wed, 2 Apr 2014 17:55:04 +0000 (13:55 -0400)]
working on sra and get.mimarkspackage commands.  added file parameter to cluster.split command. seq. error not saving current fasta anymore. sffinfo and fastq.info using “ignore” feature to play nicely with sra command.

4 years agoworking of get.mimarkspackage and sra command
Sarah Westcott [Tue, 1 Apr 2014 18:13:11 +0000 (14:13 -0400)]
working of get.mimarkspackage and sra command

4 years agochanged int to pid_t type in fork(). roughed in get.mimarkscommand.
Sarah Westcott [Tue, 25 Mar 2014 13:18:32 +0000 (09:18 -0400)]
changed int to pid_t type in fork(). roughed in get.mimarkscommand.

4 years agoadded mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change...
Sarah Westcott [Tue, 25 Mar 2014 12:30:35 +0000 (08:30 -0400)]
added mothurgetpid function. fixed bug with align.seqs related to g++ 4.8 change.  fixed bug in rarefaction.single with shared command if shared file not created by mothur labels not in right order in *.groups.rarefaction. summary.shared sub ample bug, not subampleing. added rjsd and jsd to tree.shared. working on sra command. chimera.slayer blast error bug on linux related to getpid().

4 years agoadded shared file to make.table
Sarah Westcott [Thu, 6 Mar 2014 16:51:27 +0000 (11:51 -0500)]
added shared file to make.table

4 years agoadded shannonrange calc.
Sarah Westcott [Wed, 5 Mar 2014 19:32:31 +0000 (14:32 -0500)]
added shannonrange calc.

4 years agopcr.seqs bug fix. working on shannon range calc
Sarah Westcott [Fri, 28 Feb 2014 19:59:14 +0000 (14:59 -0500)]
pcr.seqs bug fix.  working on shannon range calc

4 years agofixed bug in make.biom with picrust that didn’t allow for unclassified OTUs. fixed...
Sarah Westcott [Tue, 25 Feb 2014 16:57:05 +0000 (11:57 -0500)]
fixed bug in make.biom with picrust that didn’t allow for unclassified OTUs. fixed bug in fastq.info that quit after 100000 seqs

5 years agofixes while building
Sarah Westcott [Wed, 12 Feb 2014 16:40:10 +0000 (11:40 -0500)]
fixes while building

5 years agofixing help
Sarah Westcott [Tue, 11 Feb 2014 19:56:14 +0000 (14:56 -0500)]
fixing help

5 years agofixes while testing 1.33.0
Sarah Westcott [Mon, 10 Feb 2014 13:22:57 +0000 (08:22 -0500)]
fixes while testing 1.33.0

5 years agoadded relabund parameter to classify.seqs and summary.tax commands
Sarah Westcott [Tue, 4 Feb 2014 17:49:53 +0000 (12:49 -0500)]
added relabund parameter to classify.seqs and summary.tax commands

5 years agoadded mergesfffiles command. added current directories to get.current commands output...
Sarah Westcott [Mon, 3 Feb 2014 21:26:20 +0000 (16:26 -0500)]
added mergesfffiles command. added current directories to get.current commands outputs.  modified deunique.seqs output filename creation.

5 years agofixed bug in pam
Sarah Westcott [Fri, 31 Jan 2014 16:22:42 +0000 (11:22 -0500)]
fixed bug in pam

5 years agoworking on get.communitytype command
Sarah Westcott [Wed, 29 Jan 2014 21:03:17 +0000 (16:03 -0500)]
working on get.communitytype command

5 years agoadded rjsd calculator. improved work balance load between processors for paralellize...
Sarah Westcott [Tue, 21 Jan 2014 20:26:12 +0000 (15:26 -0500)]
added rjsd calculator.  improved work balance load between processors for paralellized commands: metastats, unifrac.weighted, unifrac.unweighted, parsimony, chimera.uchime, chimera.perseus, chimera.slayer, shhh.seqs and pre.cluster.

5 years agoMerge remote-tracking branch 'origin/master'
Sarah Westcott [Tue, 21 Jan 2014 15:58:16 +0000 (10:58 -0500)]
Merge remote-tracking branch 'origin/master'

5 years agoworking on pam
Sarah Westcott [Tue, 21 Jan 2014 15:58:06 +0000 (10:58 -0500)]
working on pam

5 years agoTest new machine.
Sarah Westcott [Tue, 21 Jan 2014 02:23:45 +0000 (21:23 -0500)]
Test new machine.

5 years agoconverted jsd calculation to be based on relative abundance
Pat Schloss [Thu, 9 Jan 2014 15:34:03 +0000 (10:34 -0500)]
converted jsd calculation to be based on relative abundance

5 years agoMerge remote-tracking branch 'mothur/master'
Pat Schloss [Thu, 9 Jan 2014 14:57:02 +0000 (09:57 -0500)]
Merge remote-tracking branch 'mothur/master'

5 years agoadded Jensen-Shannon calc. working on get.communitytype command. fixed bug in get...
Sarah Westcott [Thu, 9 Jan 2014 14:44:50 +0000 (09:44 -0500)]
added Jensen-Shannon calc. working on get.communitytype command.  fixed bug in get.oturep command with count file. fixed bug in trim.flows that caused issue when you read back in scrap flow file.  added log transform parameter to trims.seqs command and allow non paired barcodes and primers to use reorient. fixed bug in lefse when kruskal returned nan.

5 years agoMerge remote-tracking branch 'mothur/master'
Pat Schloss [Wed, 8 Jan 2014 22:17:38 +0000 (17:17 -0500)]
Merge remote-tracking branch 'mothur/master'

5 years agosome changes on qFinderDMM
Pat Schloss [Wed, 8 Jan 2014 22:17:22 +0000 (17:17 -0500)]
some changes on qFinderDMM

5 years agoadded oligos, group, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs to fastq.info so you...
Sarah Westcott [Tue, 3 Dec 2013 19:51:46 +0000 (14:51 -0500)]
added oligos, group, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs to fastq.info so you can parse fastq files by sample.  added group file to sffinfo so you can parse by group. added parsing to sra command.

5 years agotypo
Sarah Westcott [Tue, 19 Nov 2013 17:16:41 +0000 (12:16 -0500)]
typo

5 years agoadded binary file operations to mothurout class. added comment to sequence class...
Sarah Westcott [Tue, 19 Nov 2013 17:15:21 +0000 (12:15 -0500)]
added binary file operations to mothurout class. added comment to sequence class. permute parameter can equal 1, 2, 3, or 4 in venn command. fixed bug with sffinfo in windows with oligos file. fixed bug with summary.shared processors > 1 subsample=t, caused *ave.dist matrix values = 0. made make.biom picrust compliant. added binLabels to get.oturep command. added count file to deunique.seqs command. set.current was overwriting processors. fixed bug with pcr.seqs and aligned templates. added "group" column header to nods axes file. changed bayesian to wang in classify.seqs header. added warning about using count file with self reference in chimera.uchime.

5 years agoadded picrust and ref taxonomy parameters to make.biom
Sarah Westcott [Tue, 22 Oct 2013 12:25:55 +0000 (08:25 -0400)]
added picrust and ref taxonomy parameters to make.biom

5 years agomodifications to commands to add headers to list file.
Sarah Westcott [Fri, 18 Oct 2013 18:34:29 +0000 (14:34 -0400)]
modifications to commands to add headers to list file.

5 years agoMerge remote-tracking branch 'origin/master'
Sarah Westcott [Thu, 17 Oct 2013 18:20:45 +0000 (14:20 -0400)]
Merge remote-tracking branch 'origin/master'

5 years agoadding labels to list file.
Sarah Westcott [Thu, 17 Oct 2013 18:20:30 +0000 (14:20 -0400)]
adding labels to list file.

5 years agoadded fastq to list.seqs, get.seqs and remove.seqs. fixed bug where venn command...
Sarah Westcott [Thu, 17 Oct 2013 17:45:05 +0000 (13:45 -0400)]
added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where venn command overwrote sharedotus files. fixed bug with sff.multiple setting processors=1 for future commands. Not using file redirects in commands it runs.

5 years agoadded otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and OTU001 are...
Sarah Westcott [Tue, 8 Oct 2013 18:33:50 +0000 (11:33 -0700)]
added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and OTU001 are recognized as the same. fixed bug with chimera commands and count table with dereplicate=t. fixed compile issue with shhh.flows command in MPI version

5 years agochanges while testing
Sarah Westcott [Wed, 2 Oct 2013 11:23:27 +0000 (07:23 -0400)]
changes while testing

5 years agoMerge remote-tracking branch 'origin'
Sarah Westcott [Wed, 18 Sep 2013 16:54:25 +0000 (12:54 -0400)]
Merge remote-tracking branch 'origin'

5 years agoadded lefse command. added check for hard filter length. fixed bug in make.biom...
Sarah Westcott [Wed, 18 Sep 2013 16:53:47 +0000 (12:53 -0400)]
added lefse command. added check for hard filter length.  fixed bug in make.biom when multiple labels in shared file. added index file to make.contigs. fixed weird output in summary.seqs for mean values. added checks for edianness in sffinfo when oligos file is used. shhh.flows fix for reads longer than 1024. fixed bug in split.groups with count file. added several functions to linearalegra for lefse.

5 years agochanging command name classify.shared to classifyrf.shared
Kathryn Iverson [Mon, 16 Sep 2013 14:18:12 +0000 (10:18 -0400)]
changing command name classify.shared to classifyrf.shared

5 years agoadding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:42:26 +0000 (14:42 -0400)]
adding misclassification output file

5 years agoadding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:42 +0000 (14:41 -0400)]
adding misclassification output file

5 years agoadding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:35 +0000 (14:41 -0400)]
adding misclassification output file

5 years agoadding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:27 +0000 (14:41 -0400)]
adding misclassification output file

5 years agoadding pretty confusion matrix
kdiverson [Wed, 11 Sep 2013 15:28:17 +0000 (11:28 -0400)]
adding pretty confusion matrix

5 years agoadding pretty confusion matrix
kdiverson [Wed, 11 Sep 2013 15:27:58 +0000 (11:27 -0400)]
adding pretty confusion matrix

5 years agoadding code for confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:45 +0000 (00:48 -0400)]
adding code for confusion matrix

5 years agoadding code for confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:35 +0000 (00:48 -0400)]
adding code for confusion matrix

5 years agoadding code for confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:20 +0000 (00:48 -0400)]
adding code for confusion matrix

5 years agochanged random forest output filename
kdiverson [Tue, 10 Sep 2013 13:52:01 +0000 (09:52 -0400)]
changed random forest output filename

5 years agoMerge remote-tracking branch 'mothur/master'
Pat Schloss [Wed, 4 Sep 2013 21:36:24 +0000 (17:36 -0400)]
Merge remote-tracking branch 'mothur/master'

5 years agorandom stuff
Pat Schloss [Wed, 4 Sep 2013 21:35:47 +0000 (17:35 -0400)]
random stuff

5 years agoMerge remote-tracking branch 'origin'
Sarah Westcott [Wed, 14 Aug 2013 16:20:47 +0000 (12:20 -0400)]
Merge remote-tracking branch 'origin'

5 years agochanged name of get.metacommunity to get.communitytype. fixed bug in metastats comman...
Sarah Westcott [Wed, 14 Aug 2013 16:20:04 +0000 (12:20 -0400)]
changed name of get.metacommunity to get.communitytype. fixed bug in metastats command with low frequency OTUs. fisher[1] instead of fisher[i]. working on lefse command. fixed sffinfo index offset value when oligos file is used. changed default lookup file location.

5 years agoMerge remote-tracking branch 'origin'
Sarah Westcott [Fri, 2 Aug 2013 12:43:49 +0000 (08:43 -0400)]
Merge remote-tracking branch 'origin'

5 years agoQualscore gobbles
Sarah Westcott [Fri, 2 Aug 2013 12:43:17 +0000 (08:43 -0400)]
Qualscore gobbles

5 years agoUpdate mgcluster to use dist=1 for missing distances when no cutoff is provided.
Pat Schloss [Fri, 19 Jul 2013 11:35:44 +0000 (07:35 -0400)]
Update mgcluster to use dist=1 for missing distances when no cutoff is provided.

5 years agoadded adjust parameter to mgcluster. fixed bug in classify.otu with countable. fixed...
Sarah Westcott [Thu, 18 Jul 2013 20:16:16 +0000 (13:16 -0700)]
added adjust parameter to mgcluster. fixed bug in classify.otu with countable. fixed bug in otu.heirarchy with otulabels.  fixed bug with summary.seqs overflow when calculating the mean values.

5 years agoasdf
Pat Schloss [Wed, 17 Jul 2013 18:56:23 +0000 (14:56 -0400)]
asdf

5 years agoMerge remote-tracking branch 'mothur/master'
Pat Schloss [Wed, 17 Jul 2013 18:52:16 +0000 (14:52 -0400)]
Merge remote-tracking branch 'mothur/master'

5 years agofixed problem where order=B was not checking for the maximum homopolymer length
Pat Schloss [Wed, 17 Jul 2013 18:51:48 +0000 (14:51 -0400)]
fixed problem where order=B was not checking for the maximum homopolymer length

5 years agoMerge remote-tracking branch 'origin'
Sarah Westcott [Mon, 24 Jun 2013 18:32:11 +0000 (14:32 -0400)]
Merge remote-tracking branch 'origin'

5 years agoadded kruskal.wallis command. added worked on make.lefse. working of lefse command...
Sarah Westcott [Mon, 24 Jun 2013 18:31:29 +0000 (14:31 -0400)]
added kruskal.wallis command. added worked on make.lefse. working of lefse command. fixed bug in trim.oligos when there was an exact match to paired primers or barcodes that overlapped causing the sequence to be shorter than the barcodes and primers.  added design map class. added kruskal wallis and wilcoxon functions to linear algebra class.

5 years agotest change
John Westcott [Mon, 24 Jun 2013 18:19:31 +0000 (14:19 -0400)]
test change

5 years agomgcluster with count file needed to create a nameMap to pass to readBlast like the...
Sarah Westcott [Thu, 13 Jun 2013 18:35:45 +0000 (14:35 -0400)]
mgcluster with count file needed to create a nameMap to pass to readBlast like the name file does

5 years agoadded make.lefse command. fixed bug in make.contigs with trimming reverse barcodes...
Sarah Westcott [Thu, 13 Jun 2013 14:52:30 +0000 (10:52 -0400)]
added make.lefse command.  fixed bug in make.contigs with trimming reverse barcodes and primers. removed extra names check from classfier.  changed minlength default in trim.seqs to 1. added readConsTax function to mothurOut

5 years agoget.seqs not renaming sequences correctly for dups=f. unique.seqs crash when count...
Sarah Westcott [Wed, 29 May 2013 18:16:43 +0000 (14:16 -0400)]
get.seqs not renaming sequences correctly for dups=f. unique.seqs crash when count table had group data.

5 years agoadded rename.seqs command.
Sarah Westcott [Wed, 29 May 2013 12:11:22 +0000 (08:11 -0400)]
added rename.seqs command.

5 years agocase sensitive include statement caused issues for Unix systems.
Sarah Westcott [Tue, 28 May 2013 17:11:45 +0000 (13:11 -0400)]
case sensitive include statement caused issues for Unix systems.

5 years agocitation changes for 1.31.0
Sarah Westcott [Tue, 28 May 2013 13:45:57 +0000 (09:45 -0400)]
citation changes for 1.31.0

5 years agoMerge remote-tracking branch 'origin'
Sarah Westcott [Fri, 24 May 2013 14:16:22 +0000 (10:16 -0400)]
Merge remote-tracking branch 'origin'

5 years agoadded debugging to otu.association
Sarah Westcott [Fri, 24 May 2013 14:15:59 +0000 (10:15 -0400)]
added debugging to otu.association

5 years agore-enabling the destructor to enable deletion of dynamically allocated memory.
Abu Zaher Md. Faridee [Thu, 23 May 2013 21:50:24 +0000 (03:50 +0600)]
re-enabling the destructor to enable deletion of dynamically allocated memory.

5 years agoMerge branch 'master' into dev-ml
Abu Zaher Md. Faridee [Thu, 23 May 2013 21:17:06 +0000 (03:17 +0600)]
Merge branch 'master' into dev-ml

5 years agochanges while testing
Sarah Westcott [Thu, 23 May 2013 17:09:25 +0000 (13:09 -0400)]
changes while testing

5 years agochanged how rarefaction commands find the lci and hci. they now save values from...
Sarah Westcott [Fri, 17 May 2013 18:44:40 +0000 (14:44 -0400)]
changed how rarefaction commands find the lci and hci. they now save values from each iter at each frequency, report values at the .025 and .975.

5 years agoadded modify names parameter to set.dir
Sarah Westcott [Fri, 17 May 2013 13:47:21 +0000 (09:47 -0400)]
added modify names parameter to set.dir

5 years agoupdated default parameters. These are giving better error rates.
Kathryn Iverson [Thu, 16 May 2013 15:09:48 +0000 (11:09 -0400)]
updated default parameters. These are giving better error rates.

5 years agocleaned up what is printed to screen
Kathryn Iverson [Thu, 16 May 2013 14:50:21 +0000 (10:50 -0400)]
cleaned up what is printed to screen

5 years agoadded make.lookup command.
Sarah Westcott [Wed, 15 May 2013 13:49:03 +0000 (09:49 -0400)]
added make.lookup command.

5 years agoadded count file to create.database command. corrected for change to get.oturep chang...
Sarah Westcott [Tue, 14 May 2013 12:14:36 +0000 (08:14 -0400)]
added count file to create.database command. corrected for change to get.oturep changing order of members in otu to reflect the names file format.  That change caused the create.database command to fail to find otus

5 years agocluster.split was not sorting the list file in order of abundance
Sarah Westcott [Mon, 13 May 2013 15:34:21 +0000 (11:34 -0400)]
cluster.split was not sorting the list file in order of abundance

5 years agoadded sparcc command. fixed bug in remove.groups that removed all groups if you...
Sarah Westcott [Mon, 13 May 2013 15:05:36 +0000 (11:05 -0400)]
added sparcc command.  fixed bug in remove.groups that removed all groups if you had a typo in the group name. fixed order parameter in sff.multiple.

5 years agoparalellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for...
Sarah Westcott [Mon, 6 May 2013 19:08:59 +0000 (15:08 -0400)]
paralellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for windows.

5 years agoa lot of new input parameters in rf module, implemented a pruning system in the rf...
Abu Zaher Md. Faridee [Thu, 2 May 2013 16:30:45 +0000 (22:30 +0600)]
a lot of new input parameters in rf module, implemented a pruning system in the rf tree plus some runtime performance improvements

5 years agoadded square format for phylipfile. made command work with list files containing...
SarahsWork [Mon, 29 Apr 2013 18:55:14 +0000 (14:55 -0400)]
added square format for phylipfile. made command work with list files containing unique and redundant sequences

5 years agoadded shared, constaxonomy and label parameter to get.lineage and remove.lineage...
SarahsWork [Mon, 29 Apr 2013 15:58:15 +0000 (11:58 -0400)]
added shared, constaxonomy and label parameter to get.lineage and remove.lineage commands. Allows user to select / remove OTUs that classified to a specific taxonomy or set of taxonomies.

5 years agoadded adjustDots function to pcr.seqs, keeps sequences aligned in case where primers...
SarahsWork [Fri, 26 Apr 2013 13:25:37 +0000 (09:25 -0400)]
added adjustDots function to pcr.seqs, keeps sequences aligned in case where primers are found at different locations.

5 years agoparalellized make.table / count.seqs command. added getCopy function to groupMap...
SarahsWork [Mon, 22 Apr 2013 17:23:06 +0000 (13:23 -0400)]
paralellized make.table / count.seqs command. added getCopy function to groupMap class.

5 years agoadded flag to count table read so that commands that don't require the group info...
SarahsWork [Mon, 22 Apr 2013 13:47:08 +0000 (09:47 -0400)]
added flag to count table read so that commands that don't require the group info can tell countTable to ignore it

5 years agoadded mothurOutJustToScreen function and changed all counter outputs to use it.
SarahsWork [Fri, 19 Apr 2013 18:19:00 +0000 (14:19 -0400)]
added mothurOutJustToScreen function and changed all counter outputs to use it.

5 years agoparalellized unifrac.weighted for windows. added get.metacommunity command. fixed...
SarahsWork [Fri, 19 Apr 2013 13:37:01 +0000 (09:37 -0400)]
paralellized unifrac.weighted for windows. added get.metacommunity command.  fixed bug in sequence class filterToPos that was effecting pcr.seqs trimming. {For forward primer trimming with aligned sequences and keepdots=t. If the character before the first primer base was a base and not a gap the base was not trimmed.} modified setFilePosFasta in mothurOut class to help with large files on 32bit machines.

5 years agoadded get.metacommunity command.
SarahsWork [Fri, 12 Apr 2013 17:52:41 +0000 (13:52 -0400)]
added get.metacommunity command.

5 years agoadded rarepercent and keepties parameters to the filter.shared command.
SarahsWork [Mon, 8 Apr 2013 16:48:26 +0000 (12:48 -0400)]
added rarepercent and keepties parameters to the filter.shared command.

5 years agoadded method parameter to get.oturep. options method=abundance or distance. default...
SarahsWork [Fri, 5 Apr 2013 19:05:44 +0000 (15:05 -0400)]
added method parameter to get.oturep. options method=abundance or distance. default=distance. added summary type to current types saved by mother

5 years agosffinfo bug with flow grams right index when clipQualRight=0
SarahsWork [Fri, 5 Apr 2013 12:44:08 +0000 (08:44 -0400)]
sffinfo bug with flow grams right index when clipQualRight=0

5 years agoadded name, group and count files to chop.seqs. added intelligent warnings for when...
SarahsWork [Wed, 3 Apr 2013 18:56:23 +0000 (14:56 -0400)]
added name, group and count files to chop.seqs. added intelligent warnings for when you use a group file instead of design file - common bug report.

5 years agoadded count file to get.sabund and get.rabund commands. fixed bug in windows paralell...
SarahsWork [Wed, 3 Apr 2013 15:03:57 +0000 (11:03 -0400)]
added count file to get.sabund and get.rabund commands. fixed bug in windows paralellization of pairwise.seqs - cutoff was not passed to thread. added otulabels to shared file in remove.rare command.  added check to make sure reorient is only used when paired barcodes are provided.

5 years agoadded end of file character to some type type reads. fixes while testing.
SarahsWork [Mon, 1 Apr 2013 11:43:39 +0000 (07:43 -0400)]
added end of file character to some type type reads. fixes while testing.

5 years agoremoved make count from make.contigs
SarahsWork [Mon, 25 Mar 2013 13:01:02 +0000 (09:01 -0400)]
removed make count from make.contigs