John Westcott [Wed, 9 May 2012 15:31:46 +0000 (11:31 -0400)]
added debug flag to mothurOut. added debug parameter to set.dir. added debug code to catchall and get.seqs commands. created newcommandtemplate. started work on get.coremicrobiom command. fixed command parameter bug in chimera.bellerophon command.
Sarah Westcott [Wed, 2 May 2012 19:22:40 +0000 (15:22 -0400)]
fixed segfault in unifrac with subsample. in progress of implementing a version of the subsample tree that sets sees you don't want to includes groups to doNotIncludeMe. to test which is more efficient.
removed initmatrix and replaced it with co_matrix. With the re-written command there shouldn't be a need to keep the initial matrix, it's just taking up memory.
Sarah Westcott [Wed, 11 Apr 2012 15:35:07 +0000 (11:35 -0400)]
fixed bug with windows version of trim.seqs when run with 1 processor. fixed file output redirect for shhh.slows command. modified mothur so that you can set input and output directories using the parameters in the command.
Sarah Westcott [Thu, 5 Apr 2012 13:52:08 +0000 (09:52 -0400)]
added subsample, tiers and processors to tree.shared command. removed bootstrap.shared command. converted consensus command to a class. fixed a few small things related to binLabels.
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.
projects / mothur.git / log