Sarah Westcott [Mon, 2 Apr 2012 14:14:38 +0000 (10:14 -0400)]
added create.database command. fixed help in get.sharedseqs. added new constructor to sequence class to get comment strings after sequence name. fixed filenames in sffinfo when sff file did not end in .sff. removed debugging c out statement from trim.flows.
Sarah Westcott [Tue, 27 Mar 2012 16:35:08 +0000 (12:35 -0400)]
added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error if group names contained '_' in shared file. metastats - modified to more closely follow results from metastats website. trim.flows and trim.seqs allow for characters other than ATGC in reverse primers. removed name file warning when mother calls command internally.
Sarah Westcott [Tue, 6 Mar 2012 12:54:36 +0000 (07:54 -0500)]
changed sffinfo flow default to true. fixed bug in trim.seqs and filter.seqs related to windows paralellization mods, added help and description to concurrence command
Sarah Westcott [Mon, 5 Mar 2012 14:59:50 +0000 (09:59 -0500)]
fixed classify.seq error message when flip accnos file was blank. Fixed bug with phylotype command related to the addition of "unknown" classification in phylotree.
Sarah Westcott [Mon, 20 Feb 2012 20:33:22 +0000 (15:33 -0500)]
removed unused copy constructors and comments within comments that where causing nonsense warnings. Added minimum sequence length of 3 bases to correct set fault error to chimera.perseus. Fixed == bug in chop.seqs that left 'N' bases in sequence. added classify.tree command. worked on cluster.split and shhh.flows paralellization for windows, not complete. optimized shhh.flows paralellzation for mac and linux. added linker and spacer options to oligos file of trim.seqs. added ldiffs and sdiffs to allow for differences in linker and spacers in trim.seqs. added keepforward to trim.seqs to allow for keeping the forward primer.
Sarah Westcott [Mon, 6 Feb 2012 20:29:09 +0000 (15:29 -0500)]
added flow file to sort.seqs. added setName and setScores functions to Quality Scores, similar to sequence class. modified trim.flows so that it outputs the fullpathname to the .flow.files file. changed nods command so that if (maxdim < mindim) { maxdim = mindim; }, removing warning and abort.
Sarah Westcott [Mon, 6 Feb 2012 18:46:47 +0000 (13:46 -0500)]
added sort.seqs command. puts sequences from a fasta, name, group, quality or taxonomy file in the same order. may provide a accnos file it you wish to specify order used. large parameter can be set to true if the fasta or qfile is too large to fit in memory.
westcott [Wed, 25 Jan 2012 15:09:47 +0000 (10:09 -0500)]
added otu.association command. added calcSpearman, calcKendall and calcPearson functions to linear algebra classes to allow for passing single dimension vectors.
westcott [Thu, 19 Jan 2012 12:44:14 +0000 (12:44 +0000)]
fixed bug with shhh.flow from file path name in write functions, added "smart" feature with namefile, added fasta and qfile parameters to fastq.info, added checking for reverse sequences in classifier.
westcott [Mon, 14 Nov 2011 20:28:59 +0000 (20:28 +0000)]
finished shhh.seqs command, fixed bug with remove.groups and get.groups that caused file mismatch if column 1 of the names file was not chosen, added warning to sequence class about protein sequences.
westcott [Fri, 11 Nov 2011 14:17:31 +0000 (14:17 +0000)]
fixed bug with trim.flows that was adding flow files names to the .flow.files file more than once. working on shhh.seqs command, finished chimera.perseus command. Fixed bug with chimera.uchime relating to uchime executable location. added column headings to chimera.uchime output.
westcott [Mon, 7 Nov 2011 16:22:50 +0000 (16:22 +0000)]
working on chimera.perseus. made removeConfidences function smarter. Fixed bug in mothurmetastats.cpp that stemmed from the original source. Indexes were off, became noticeable because we sort group names.
westcott [Mon, 24 Oct 2011 11:53:53 +0000 (11:53 +0000)]
added processors to pre.cluster for mac and windows. Fixed bug in reNameFile function in mothurOut that prevented Windows from renaming the file. If user runs cluster with a phylip formatted distance file and no cutoff, use cluster.classic to save memory and time.
working on windows paralellization, added trimOligos class to be used by trim.flows and trim.seqs commands. Added sequenceParser class to divide fasta and names files by group. Added group and bygroup options to pre.cluster to allow you to pre.cluster within each group.
westcott [Mon, 22 Aug 2011 19:10:08 +0000 (19:10 +0000)]
added multiple processors option for Windows users to align.seqs, dist.seqs, summary.seqs. forced mothurOut, groupmap and treemap groups to be private so we can force the order to be sorted
rewrote metastats command in c++, added mothurRemove function to handle ~ error. fixed bug with classify.otu summary file. added check for isnum in quality scores read.
added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error commands. added clear.memory command. added error message to chimera.slayer and chimera.uchime to avoid user entering both a namefile and reference file.
projects / mothur.git / log