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.
Sarah Westcott [Mon, 11 Jun 2012 16:13:55 +0000 (12:13 -0400)]
fixed bug with dist.shared subsampling. added mode parameter to dist.shared so you can select average or median for the results. added some debug code as I sorted out some bug reports to mothur.bugs.
Sarah Westcott [Mon, 4 Jun 2012 19:40:50 +0000 (15:40 -0400)]
fixed classify.seqs output file name - had issue if reference taxonomy file did not have 3 parts to the name. modified rarefaction.shared to output a group.rarefaction file when design file is used.
Sarah Westcott [Mon, 4 Jun 2012 16:27:23 +0000 (12:27 -0400)]
added check to make sure shhh.flows child processes finish properly. added subsampling to summary.shared and summary.single. modified dist.shared to run original dataset as well as subsamples when subsample=t
Sarah Westcott [Thu, 24 May 2012 16:50:47 +0000 (12:50 -0400)]
fixed bug in sffinfo when ~ was used in the sff filename. fixed issue in shhh.flows, it was producing an output file called *.flow.fasta instead of *.fasta. Also when using outputdir with the file option, it put the shhh.fasta and shhh.names files in the wrong folder. changed format of rarefaction.single output with groups to look more like the phylo.diversity command.
Sarah Westcott [Fri, 18 May 2012 16:35:51 +0000 (12:35 -0400)]
added check to cluster.classic to make sure file type is phylip. added mapping function to alignments traceback function so we can relate the position in the unaligned sequence to the aligned sequence. worked on make.contigs command
Sarah Westcott [Tue, 15 May 2012 17:54:41 +0000 (13:54 -0400)]
added list.labels command. started work on make.contigs command. fixed fastq.info and make.fastq quality scores control character. fixed bug in classify.otu that made bootstrap values for "unknown" taxon too high
projects / mothur.git / log