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 17:15:21 +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 [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, 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.
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 [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.
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.
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 [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
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.
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.
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.
SarahsWork [Mon, 18 Mar 2013 17:36:59 +0000 (13:36 -0400)]
working on dereplicate=t issue in chimera.slayer and chimera.perseus, added appendFilesWithoutHeaders to mothurOut. fixed bug in make.contigs with headers. fixed name file overwrite in unique.seqs. fixed seq name mismatch in get.seqs if dups=f. added count file to seq. error command.
SarahsWork [Tue, 5 Mar 2013 19:13:00 +0000 (14:13 -0500)]
working on chimera.uchime change for dereplicate=t bug. added shared file to get.shareseqs command and changed groups parameters to shared groups and unique groups. fixed trimming bug with trim.flows. working on trim.seqs for paired barcodes.
SarahsWork [Wed, 27 Feb 2013 20:08:18 +0000 (15:08 -0500)]
mods to resolve some misc warnings. added alignPrimer function to needle man to allow for degenerated bases. added trimming of paired barcodes and primers to trim.seqs