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
Sarah Westcott [Tue, 12 Feb 2013 20:36:52 +0000 (15:36 -0500)]
added order=A or order=B to trim.flows and shhh.flows commands. added load balancing based on flow file size to shhh.flows. fixed bug in tree.shared subsampling. fixed bug in pcr.seqs with aligned files using both forward and reverse primers.
Sarah Westcott [Mon, 11 Feb 2013 12:14:38 +0000 (07:14 -0500)]
added ':' name check to seq. error and fastq.info. sffinfo now ignores clipQualRight values of 0. fixed bug in pcr.seqs if file was aligned and both forward and reverse primers were given, reverse primer was not trimmed properly. added pdiffs to pcr.seqs.
Sarah Westcott [Wed, 6 Feb 2013 16:44:10 +0000 (11:44 -0500)]
added *.count.summary file to count.groups command. added deltaq and insert parameters to make.contigs and changed contigs.report file. added illumina1.8+ format to fast commands. added contigsreport, align report and summary files to screen.seqs to allow files to be screened using their inputs. added minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim parameters to screen.seqs. added optimization types of minoverlap, ostart, oend, mismatches, maxn, minscore,maxinsert, minsim to screen.seqs. added getNumNs function to sequence class. working on Windows \\ issue.
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.
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