Bug Fix: learnErrors and filterAndTrim arguments

The compress argument for filterAndTrim, and the
errorEstimationFunction argument for learnErrors, are now properly used.

DESCRIPTION

@@ -7,7 +7,7 @@ Description: The dada2 package infers exact sequence variants (SVs) from amplico
     and their sample-wise abundances after removing substitution and chimera
     errors. Taxonomic classification is available via a native implementation
     of the RDP naive Bayesian classifier.
-Version: 1.4.0
+Version: 1.4.1
 Date: 2017-04-24
 Maintainer: Benjamin Callahan <[email protected]>
 Author: Benjamin Callahan <[email protected]>, Paul McMurdie, Susan

NEWS

@@ -1,3 +1,13 @@
+CHANGES IN VERSION 1.4.1
+-----------------------
+
+BUG FIXES
+
+    o filterAndTrim now respects the compress argument.
+
+    o learnErrors now respects the errorEstimationFunction argument.
+
+
 CHANGES IN VERSION 1.3.5
 -----------------------
 

R/errorModels.R

@@ -83,10 +83,8 @@ loessErrfun <- function(trans) {
 #'  
 #' @param errorEstimationFunction (Optional). Function. Default \code{\link{loessErrfun}}.
 #' 
-#'  If USE_QUALS = TRUE, \code{errorEstimationFunction} is computed on the matrix of observed transitions
+#'  \code{errorEstimationFunction} is computed on the matrix of observed transitions
 #'  after each sample inference step in order to generate the new matrix of estimated error rates.
-#'    
-#'  If USE_QUALS = FALSE, this argument is ignored, and transition rates are estimated by maximum likelihood (t_ij = n_ij/n_i).
 #'  
 #' @param multithread (Optional). Default is FALSE.
 #'  If TRUE, multithreading is enabled and the number of available threads is automatically determined.   
@@ -133,7 +131,7 @@ learnErrors <- function(fls, nreads=1e6, errorEstimationFunction = loessErrfun,
   }
   drps <- drps[1:i]
   # Run dada in self-consist mode on those samples
-  dds <- dada(drps, err=NULL, selfConsist=TRUE, multithread=multithread)
+  dds <- dada(drps, err=NULL, selfConsist=TRUE, errorEstimationFunction=errorEstimationFunction, multithread=multithread)
   cat("Total reads used: ", NREADS, "\n")
   return(getErrors(dds, detailed=TRUE))
 }

R/filter.R

@@ -181,14 +181,15 @@ filterAndTrim <- function(fwd, filt, rev=NULL, filt.rev=NULL, compress=TRUE,
                      mapply(c, fwd, rev, SIMPLIFY=FALSE), mapply(c, filt, filt.rev, SIMPLIFY=FALSE), 
                      MoreArgs = list(truncQ=truncQ, truncLen=truncLen, trimLeft=trimLeft, maxLen=maxLen, minLen=minLen,
                                      maxN=maxN, minQ=minQ, maxEE=maxEE, rm.phix=rm.phix, primer.fwd=primer.fwd,
-                                     matchIDs=matchIDs, id.sep=id.sep, id.field=id.field, n=n, OMP=OMP, verbose=verbose),
+                                     matchIDs=matchIDs, id.sep=id.sep, id.field=id.field, n=n, OMP=OMP, 
+                                     compress=compress, verbose=verbose),
                      mc.cores=ncores, mc.silent=TRUE)
   } else {
     rval <- mcmapply(fastqFilter, 
                      fwd, filt, 
                      MoreArgs = list(truncQ=truncQ, truncLen=truncLen, trimLeft=trimLeft, maxLen=maxLen, minLen=minLen, 
                                      maxN=maxN, minQ=minQ, maxEE=maxEE, rm.phix=rm.phix, primer.fwd=primer.fwd,
-                                     n=n, OMP=OMP, verbose=verbose),
+                                     n=n, OMP=OMP, compress=compress, verbose=verbose),
                      mc.cores=ncores, mc.silent=TRUE)
   }
   colnames(rval) <- basename(fwd)

src/RcppExports.cpp

@@ -248,3 +248,27 @@ RcppExport SEXP dada2_RcppExport_registerCCallable() {
     R_RegisterCCallable("dada2", "dada2_RcppExport_validate", (DL_FUNC)dada2_RcppExport_validate);
     return R_NilValue;
 }
+
+static const R_CallMethodDef CallEntries[] = {
+    {"dada2_dada_uniques", (DL_FUNC) &dada2_dada_uniques, 19},
+    {"dada2_C_is_bimera", (DL_FUNC) &dada2_C_is_bimera, 8},
+    {"dada2_C_table_bimera2", (DL_FUNC) &dada2_C_table_bimera2, 10},
+    {"dada2_C_nwalign", (DL_FUNC) &dada2_C_nwalign, 8},
+    {"dada2_C_eval_pair", (DL_FUNC) &dada2_C_eval_pair, 2},
+    {"dada2_C_pair_consensus", (DL_FUNC) &dada2_C_pair_consensus, 4},
+    {"dada2_C_isACGT", (DL_FUNC) &dada2_C_isACGT, 1},
+    {"dada2_evaluate_kmers", (DL_FUNC) &dada2_evaluate_kmers, 6},
+    {"dada2_C_subpos", (DL_FUNC) &dada2_C_subpos, 2},
+    {"dada2_C_matchRef", (DL_FUNC) &dada2_C_matchRef, 4},
+    {"dada2_C_matrixEE", (DL_FUNC) &dada2_C_matrixEE, 1},
+    {"dada2_C_nwvec", (DL_FUNC) &dada2_C_nwvec, 7},
+    {"dada2_C_assign_taxonomy", (DL_FUNC) &dada2_C_assign_taxonomy, 7},
+    {"dada2_C_assign_taxonomy2", (DL_FUNC) &dada2_C_assign_taxonomy2, 7},
+    {"dada2_RcppExport_registerCCallable", (DL_FUNC) &dada2_RcppExport_registerCCallable, 0},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_dada2(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}