Permalink
Commits on Sep 21, 2010
  1. Added alignment QC by column, clustering with ESPRIT, and fixed some …

    …bugs
    
    align2profile_qc_Col.pl
    - New file, to do alignment QC by column
    - Removes columns with coverage less than N (N=2)
    
    align2profile_qc_OnlyScore.pl
    align2profile_qc_ScoreInternalGap.pl
    - Fixed output to be "flat" (necessary for tree pruning to work)
    
    tree_to_matrix.cpp
    - added switch to print matrix (for mothur, like R version) or list (for ESPRIT input)
    - changed matrix printing to print directly to phylip rather than R format and then convert
    - added list printing format for ESPRIT
    
    OTU.pm
    - added column QC wrapper function
    - added ESPRIT clustering wrapper function
    - updated tree_to_matrix_cpp function to handle printing switches
    - updated stitch_matrix to stitch together the appropriate file types (phylip or ndist list)
    
    otu_handler.pl
    - added column QC step and corresponding variable for the cutoff)
    - added switch for clustering code (mothur or ESPRIT)
    - added tree_to_matrix printing switches
    RebeccaTruty committed Sep 21, 2010
Commits on Sep 17, 2010
  1. Added parallelized tree_to_matrix

    otu_handler.pl
    - added parallelized tree_to_matrix switch and functionality to the parallel function
    - reformatted switched and add skipto switch
    
    OTU.pm
    - added tree_to_matrix_cpp wrapper for the new c++ version of tree_to_matrix
    - added split_tree and stitch_matrix functions for parallel tree_to_matrix running
    RebeccaTruty committed Sep 17, 2010
  2. Added parallelized tree_to_matrix

    tree_to_matrix.cpp
    - New c++ code to print all or part of a tree to matrix.  Uses boost library and the PhyloTree class
    
    PhyloTree.h
    - Lightweight tree class used for reading in newick format tree before shuffling to a boost adjacency_list graph object
    
    otu_handler.pl
    - added parallelized tree_to_matrix switch and functionality to the parallel function
    - reformatted switched and add skipto switch
    
    OTU.pm
    - added tree_to_matrix_cpp wrapper for the new c++ version of tree_to_matrix
    - added split_tree and stitch_matrix functions for parallel tree_to_matrix running
    RebeccaTruty committed Sep 17, 2010
Commits on Sep 16, 2010
  1. Updated grab_SSU_reads method to enable read quality control trimming…

    … based on the best blast hit's best HSP tile (contextually linked HSPs)
    sharpton committed Sep 16, 2010
Commits on Sep 11, 2010
  1. Enable parallelized alignment QC with less restrictions

    NEW: align2profile_qc_ScoreInternalGap.pl
    - Modified align2profile_qc.pl to allow for running in parallel
    -- Remove all column-wise alignment QC (no longer removed gappy columns)
    -- Remove check on internal gaps (-sub option in infernal makes this a non-issue?)
    -- Only check the sequence length and the score per residue and the number of internal gaps
    -- Added calculation and printing of the coverage at each residue
    
    NEW: align2profile_qc_OnlyScore.pl
    - as align2profile_qc_ScoreInternalGap.pl but the internal gap check is also omitted
    
    MODIFIED: OTU.pm
    - added functionality to deal with parallel alignment QC
    -- split function extended to split both blast and alignment files
    -- stitch_alignQC function added
    
    MODIFIED: otu_handler.pl
    - added functionality to deal with parallel alignment QC
    - added switches to skip running the blast or alignment step
    RebeccaTruty committed Sep 11, 2010
Commits on Sep 10, 2010
Commits on Sep 8, 2010
Commits on Sep 7, 2010
  1. Parallelizing blast step and alignment output

    In OTU.pm
    - split_query and stitch_blast functions added to enable parallelized blasting
    - printing alignment scores immediately (helpful in diagnostics if code fails before completion)
    
    In otu_handler.pl
    - submit and parallel_blast functions added to enable parallelized blasting
    RebeccaTruty committed Sep 7, 2010
  2. Parallelizing blast step and alignment output

    - split_query and stitch_blast functions added to enable parallelized blasting
    - printing alignment scores immediately (helpful in diagnostics if code fails before completion)
    RebeccaTruty committed with Rebecca Lamb Sep 7, 2010
  3. adding core code base

    sharpton committed Sep 7, 2010
  4. first commit

    sharpton committed Sep 7, 2010