Don Armstrong [Fri, 11 Apr 2014 21:46:30 +0000 (14:46 -0700)]
fix syntax error
Don Armstrong [Fri, 11 Apr 2014 21:43:41 +0000 (14:43 -0700)]
add primary_seqname command to determine the primary sequence (first before ,)
Don Armstrong [Fri, 11 Apr 2014 19:54:04 +0000 (12:54 -0700)]
add missing +
Don Armstrong [Fri, 11 Apr 2014 19:53:26 +0000 (12:53 -0700)]
add more debugging output in printSeq
Don Armstrong [Fri, 11 Apr 2014 18:43:27 +0000 (11:43 -0700)]
handle , in outNames
Don Armstrong [Fri, 11 Apr 2014 18:38:52 +0000 (11:38 -0700)]
skip cases where scores.size is less than the base map
Don Armstrong [Fri, 11 Apr 2014 18:37:34 +0000 (11:37 -0700)]
clean up makefile
Don Armstrong [Fri, 11 Apr 2014 18:37:19 +0000 (11:37 -0700)]
use hash and file position in deconvolute
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.
Sarah Westcott [Tue, 1 Apr 2014 18:13:11 +0000 (14:13 -0400)]
working of get.mimarkspackage and sra command
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.
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().
Sarah Westcott [Thu, 6 Mar 2014 16:51:27 +0000 (11:51 -0500)]
added shared file to make.table
Sarah Westcott [Wed, 5 Mar 2014 19:32:31 +0000 (14:32 -0500)]
added shannonrange calc.
Sarah Westcott [Fri, 28 Feb 2014 19:59:14 +0000 (14:59 -0500)]
pcr.seqs bug fix. working on shannon range calc
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
Sarah Westcott [Wed, 12 Feb 2014 16:40:10 +0000 (11:40 -0500)]
fixes while building
Sarah Westcott [Tue, 11 Feb 2014 19:56:14 +0000 (14:56 -0500)]
fixing help
Sarah Westcott [Mon, 10 Feb 2014 13:22:57 +0000 (08:22 -0500)]
fixes while testing 1.33.0
Sarah Westcott [Tue, 4 Feb 2014 17:49:53 +0000 (12:49 -0500)]
added relabund parameter to classify.seqs and summary.tax commands
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.
Sarah Westcott [Fri, 31 Jan 2014 16:22:42 +0000 (11:22 -0500)]
fixed bug in pam
Sarah Westcott [Wed, 29 Jan 2014 21:03:17 +0000 (16:03 -0500)]
working on get.communitytype command
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.
Sarah Westcott [Tue, 21 Jan 2014 15:58:16 +0000 (10:58 -0500)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Tue, 21 Jan 2014 15:58:06 +0000 (10:58 -0500)]
working on pam
Sarah Westcott [Tue, 21 Jan 2014 02:23:45 +0000 (21:23 -0500)]
Test new machine.
Pat Schloss [Thu, 9 Jan 2014 15:34:03 +0000 (10:34 -0500)]
converted jsd calculation to be based on relative abundance
Pat Schloss [Thu, 9 Jan 2014 14:57:02 +0000 (09:57 -0500)]
Merge remote-tracking branch 'mothur/master'
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.
Pat Schloss [Wed, 8 Jan 2014 22:17:38 +0000 (17:17 -0500)]
Merge remote-tracking branch 'mothur/master'
Pat Schloss [Wed, 8 Jan 2014 22:17:22 +0000 (17:17 -0500)]
some changes on qFinderDMM
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.
Sarah Westcott [Tue, 19 Nov 2013 17:16:41 +0000 (12:16 -0500)]
typo
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.
Sarah Westcott [Tue, 22 Oct 2013 12:25:55 +0000 (08:25 -0400)]
added picrust and ref taxonomy parameters to make.biom
Sarah Westcott [Fri, 18 Oct 2013 18:34:29 +0000 (14:34 -0400)]
modifications to commands to add headers to list file.
Sarah Westcott [Thu, 17 Oct 2013 18:20:45 +0000 (14:20 -0400)]
Merge remote-tracking branch 'origin/master'
Sarah Westcott [Thu, 17 Oct 2013 18:20:30 +0000 (14:20 -0400)]
adding labels to list file.
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.
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
Sarah Westcott [Wed, 2 Oct 2013 11:23:27 +0000 (07:23 -0400)]
changes while testing
Sarah Westcott [Wed, 18 Sep 2013 16:54:25 +0000 (12:54 -0400)]
Merge remote-tracking branch 'origin'
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.
Kathryn Iverson [Mon, 16 Sep 2013 14:18:12 +0000 (10:18 -0400)]
changing command name classify.shared to classifyrf.shared
kdiverson [Wed, 11 Sep 2013 18:42:26 +0000 (14:42 -0400)]
adding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:42 +0000 (14:41 -0400)]
adding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:35 +0000 (14:41 -0400)]
adding misclassification output file
kdiverson [Wed, 11 Sep 2013 18:41:27 +0000 (14:41 -0400)]
adding misclassification output file
kdiverson [Wed, 11 Sep 2013 15:28:17 +0000 (11:28 -0400)]
adding pretty confusion matrix
kdiverson [Wed, 11 Sep 2013 15:27:58 +0000 (11:27 -0400)]
adding pretty confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:45 +0000 (00:48 -0400)]
adding code for confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:35 +0000 (00:48 -0400)]
adding code for confusion matrix
kdiverson [Wed, 11 Sep 2013 04:48:20 +0000 (00:48 -0400)]
adding code for confusion matrix
kdiverson [Tue, 10 Sep 2013 13:52:01 +0000 (09:52 -0400)]
changed random forest output filename
Pat Schloss [Wed, 4 Sep 2013 21:36:24 +0000 (17:36 -0400)]
Merge remote-tracking branch 'mothur/master'
Pat Schloss [Wed, 4 Sep 2013 21:35:47 +0000 (17:35 -0400)]
random stuff
Sarah Westcott [Wed, 14 Aug 2013 16:20:47 +0000 (12:20 -0400)]
Merge remote-tracking branch 'origin'
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.
Sarah Westcott [Fri, 2 Aug 2013 12:43:49 +0000 (08:43 -0400)]
Merge remote-tracking branch 'origin'
Sarah Westcott [Fri, 2 Aug 2013 12:43:17 +0000 (08:43 -0400)]
Qualscore gobbles
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.
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.
Pat Schloss [Wed, 17 Jul 2013 18:56:23 +0000 (14:56 -0400)]
asdf
Pat Schloss [Wed, 17 Jul 2013 18:52:16 +0000 (14:52 -0400)]
Merge remote-tracking branch 'mothur/master'
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
Sarah Westcott [Mon, 24 Jun 2013 18:32:11 +0000 (14:32 -0400)]
Merge remote-tracking branch 'origin'
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.
John Westcott [Mon, 24 Jun 2013 18:19:31 +0000 (14:19 -0400)]
test change
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
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
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.
Sarah Westcott [Wed, 29 May 2013 12:11:22 +0000 (08:11 -0400)]
added rename.seqs command.
Sarah Westcott [Tue, 28 May 2013 17:11:45 +0000 (13:11 -0400)]
case sensitive include statement caused issues for Unix systems.
Sarah Westcott [Tue, 28 May 2013 13:45:57 +0000 (09:45 -0400)]
citation changes for 1.31.0
Sarah Westcott [Fri, 24 May 2013 14:16:22 +0000 (10:16 -0400)]
Merge remote-tracking branch 'origin'
Sarah Westcott [Fri, 24 May 2013 14:15:59 +0000 (10:15 -0400)]
added debugging to otu.association
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.
Abu Zaher Md. Faridee [Thu, 23 May 2013 21:17:06 +0000 (03:17 +0600)]
Merge branch 'master' into dev-ml
Sarah Westcott [Thu, 23 May 2013 17:09:25 +0000 (13:09 -0400)]
changes while testing
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.
Sarah Westcott [Fri, 17 May 2013 13:47:21 +0000 (09:47 -0400)]
added modify names parameter to set.dir
Kathryn Iverson [Thu, 16 May 2013 15:09:48 +0000 (11:09 -0400)]
updated default parameters. These are giving better error rates.
Kathryn Iverson [Thu, 16 May 2013 14:50:21 +0000 (10:50 -0400)]
cleaned up what is printed to screen
Sarah Westcott [Wed, 15 May 2013 13:49:03 +0000 (09:49 -0400)]
added make.lookup command.
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
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
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.
Sarah Westcott [Mon, 6 May 2013 19:08:59 +0000 (15:08 -0400)]
paralellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for windows.
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
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
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.
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.
SarahsWork [Mon, 22 Apr 2013 17:23:06 +0000 (13:23 -0400)]
paralellized make.table / count.seqs command. added getCopy function to groupMap class.
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
SarahsWork [Fri, 19 Apr 2013 18:19:00 +0000 (14:19 -0400)]
added mothurOutJustToScreen function and changed all counter outputs to use it.
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.
SarahsWork [Fri, 12 Apr 2013 17:52:41 +0000 (13:52 -0400)]
added get.metacommunity command.
SarahsWork [Mon, 8 Apr 2013 16:48:26 +0000 (12:48 -0400)]
added rarepercent and keepties parameters to the filter.shared command.
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