Sarah Westcott [Tue, 29 Jan 2013 16:22:12 +0000 (11:22 -0500)]
added get.dists and remove.dists commands. fixed bug in trim.seqs windows paralellization that caused blank groups in group file. added list and shared file to get.otulabels and remove.otulabels. added list file to list.otulabels.
Sarah Westcott [Fri, 25 Jan 2013 20:46:33 +0000 (15:46 -0500)]
added primer.design command. fixed bug with linux unifrac subsampling, metastats output filename, venn command is no shared outs, added check for ':' in sequence names to avoid trouble with trees. added format parameter to make.contigs.
Sarah Westcott [Wed, 16 Jan 2013 16:30:18 +0000 (11:30 -0500)]
added topdown parameter to pre.cluster. added more debugging output to bayesian class. fixed mpi compile issue in cluster.split. fixed 32bit constant declarations in refchimeratest.cpp. fixed some commandName issues for gui interface
Sarah Westcott [Tue, 8 Jan 2013 17:19:41 +0000 (12:19 -0500)]
added dereplicate parameter to chimera.slayer and chimera.persues. added minnumsamples and minpercentsamples to filter.shared. fixed output names in cluster commands. added count parameter to parse.list. improved speed and memory requirements on sens.spec. added debugging code to some phylotree functions.
Sarah Westcott [Tue, 30 Oct 2012 18:04:45 +0000 (14:04 -0400)]
classify.seqs allows sequences to be in taxonomy file that are not in template. it ignores them. fixed windows bug in clearcut char* declarations. get.lineage and remove.lineage can now handle taxons with (). list vector sorts list file outs by abundance. bugs while testing
Sarah Westcott [Mon, 22 Oct 2012 15:40:41 +0000 (11:40 -0400)]
added sets to amova and homova commands. added oligos to make.contigs. added metadata to make.biom. fixed bug in get.oturep caused by adding the count file. changed vector declaration in cooccurrence to fixed windows issue. classify.seqs can now ignore seqs in taxonomy file not in template file.
Sarah Westcott [Tue, 2 Oct 2012 18:36:18 +0000 (14:36 -0400)]
added classify.shared command and random forest files. added count file to pcr.seqs, remove.rare, screen.seqs, sort.seqs, split.abund, and subsample commands
Sarah Westcott [Tue, 25 Sep 2012 13:18:08 +0000 (09:18 -0400)]
added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove.lineage and get.lineage more flexible to remove or get taxons wrapped in quotes if not given in taxon parameter.
Sarah Westcott [Fri, 7 Sep 2012 18:30:06 +0000 (14:30 -0400)]
major change to the tree class to use the count table class instead of tree map. This change involved changes to subsample class for trees, changes to the tree reader and readTree class. This change fixed bug with parsimony random tree generation that was leaving out the name file info. added count file to unifrac.unweighted, unifrac.weighted, parsimony, bin.seqs, classify.otu, classify.seqs, classify.tree, cluster.fragments, consensus.seqs, unique.seqs, phylo.diversity, summary.tax.
Sarah Westcott [Tue, 21 Aug 2012 17:39:22 +0000 (13:39 -0400)]
added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow for spitting the sff file by barcode. working on sff.multiple command.
Sarah Westcott [Mon, 30 Jul 2012 19:25:39 +0000 (15:25 -0400)]
fixed subsample name file name issue. added count parameter to cluster command. added read to readColumn and readMatrix that uses a count table. added functions to countTable class to work with clusters reads.
Sarah Westcott [Fri, 27 Jul 2012 13:42:37 +0000 (09:42 -0400)]
added sparseDistanceMatrix class. Modified cluster commands to use the new sparse distance matrix class. cut cluster time by 55% and reduced memory usage by 50%.
Sarah Westcott [Thu, 28 Jun 2012 13:37:34 +0000 (09:37 -0400)]
added countable class to read and store count file. added count parameter to make.shared command and modified sharedlistvector to use it. fixed formatting issue related to make.shared with a biom file.
Sarah Westcott [Tue, 26 Jun 2012 15:25:18 +0000 (11:25 -0400)]
made make.table alias to count.seqs command. added large parameter to count.seqs to allow for creating the table without storing files in ram. added subsampling to rarefaction.shared. added countable current type.
Sarah Westcott [Tue, 12 Jun 2012 15:27:51 +0000 (11:27 -0400)]
changed reading of name file to use buffered reads. note the splitAtWhiteSpace function is sensitive to the gobble function. do not use the two together while reading or the read can get off track. modified trim.seqs group counts to include the redundant sees if a names file is provided. changed group maps read of a group file to be buffered. modified appendFiles functions to be buffered.