* ambiguous nt warning now in verbose

BackofenLab · Mar 2, 2020 · 306d98c · 306d98c
1 parent 59a12d6
commit 306d98c
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Showing 3 changed files with 12 additions and 7 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -35,6 +35,8 @@
    * areComplementary() : 
      + check if both positions are accessible (to avoid additional checks in
        predictor recursions)
+ * bin/IntaRNA :
+   * ambiguous nt warning now in verbose log (was info log) 
 
 200217 Martin Raden
  * bin/CommandLineParsing :

diff --git a/README.md b/README.md
@@ -412,9 +412,12 @@ interaction energy = -10.85 kcal/mol
 
 ```
 
-or provide (multiple) sequence(s) in [FASTA-format](#https://en.wikipedia.org/wiki/FASTA_format).
-It is possible to provide either file input or to read the FASTA input from the
-STDIN stream.
+In case you need specific RNA names in your output, you can provide ID strings 
+for each RNA using e.g. `--tId="mRNA with GC"` or `--qId="sRNA-example"`.
+
+Multiple sequences can be provided in [FASTA-format](#https://en.wikipedia.org/wiki/FASTA_format).
+It is possible to use either file input or to read the FASTA input from the
+`STDIN` stream.
 
 ```bash
 # running IntaRNA with FASTA files
@@ -1056,7 +1059,7 @@ Finally, it is possible to restrict the overall length an interaction is allowed
 to have via `--intLenMax`. This can be done independently for the query and target sequence using
 `--qIntLenMax` and `--tIntLenMax`, respectively. By setting to 0 (default),
 the smaller of the full sequence length and the maximal accessibility-window
-size (`--tAccW`, `--qAccW`) is used.
+size is used (see `--accW`, `--tAccW`, or `--qAccW`).
 
 
 

diff --git a/src/bin/IntaRNA.cpp b/src/bin/IntaRNA.cpp
@@ -113,7 +113,7 @@ int main(int argc, char **argv){
 #if INTARNA_MULITHREADING
 						#pragma omp critical(intarna_omp_logOutput)
 #endif
-						LOG(INFO) <<"Sequence '"<<queryAccOrig->getSequence().getId()
+						VLOG(1) <<"Sequence '"<<queryAccOrig->getSequence().getId()
 								<<"' contains ambiguous nucleotide encodings. These positions are ignored for interaction computation.";
 					}
 #if INTARNA_MULITHREADING
@@ -182,8 +182,8 @@ int main(int argc, char **argv){
 #if INTARNA_MULITHREADING
 						#pragma omp critical(intarna_omp_logOutput)
 #endif
-						{ LOG(INFO) <<"Sequence '"<<targetAcc->getSequence().getId()
-								<<"' contains ambiguous IUPAC nucleotide encodings. These positions are ignored for interaction computation and replaced by 'N'.";}
+						{ VLOG(1) <<"Sequence '"<<targetAcc->getSequence().getId()
+								<<"' contains ambiguous IUPAC nucleotide encodings. These positions are ignored for interaction computation and are replaced by 'N'.";}
 					}
 
 					// second: iterate over all query sequences