follow addition of 'error.if.out.of.bounds' arg in transcriptLocs2ref…

…Locs() git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges@97944 bc3139a8-67e5-0310-9ffc-ced21a209358
RamsinghLab · Dec 31, 2014 · 8daeb93 · 8daeb93
1 parent 9e7bf11
commit 8daeb93
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Showing 4 changed files with 21 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,7 +7,7 @@ Description: The ability to efficiently represent and manipulate genomic
 	intervals. Specialized containers for representing and manipulating
 	short alignments against a reference genome are defined in the
 	GenomicAlignments package.
-Version: 1.19.26
+Version: 1.19.27
 Author: P. Aboyoun, H. Pages and M. Lawrence
 Maintainer: Bioconductor Package Maintainer <[email protected]>
 biocViews: Genetics, Infrastructure, Sequencing, Annotation, Coverage,

diff --git a/R/transcript-utils.R b/R/transcript-utils.R
@@ -17,6 +17,7 @@
 ###   o 'strand' is assumed to be a character vector with allowed values
 ###     "+" and "-" only;
 ###   o 'decreasing.rank.on.minus.strand' is assumed to be TRUE or FALSE.
+###   o 'error.if.out.of.bounds' is assumed to be TRUE or FALSE.
 
 unsafe.transcriptWidths <- function(exonStarts, exonEnds)
 {
@@ -29,12 +30,13 @@ unsafe.transcriptWidths <- function(exonStarts, exonEnds)
 ### not necessarily the "same shape") as 'exonStarts' and 'exonEnds'.
 unsafe.transcriptLocs2refLocs <- function(tlocs,
                 exonStarts, exonEnds, strand,
-                decreasing.rank.on.minus.strand)
+                decreasing.rank.on.minus.strand, error.if.out.of.bounds)
 {
     .Call2("tlocs2rlocs",
           tlocs,
           exonStarts, exonEnds, strand,
           decreasing.rank.on.minus.strand,
+          error.if.out.of.bounds,
           PACKAGE="GenomicRanges")
 }
 
diff --git a/src/R_init_GenomicRanges.c b/src/R_init_GenomicRanges.c
@@ -7,7 +7,7 @@ static const R_CallMethodDef callMethods[] = {
 
 /* transcript_utils.c */
 	CALLMETHOD_DEF(transcript_widths, 2),
-	CALLMETHOD_DEF(tlocs2rlocs, 5),
+	CALLMETHOD_DEF(tlocs2rlocs, 6),
 
 	{NULL, NULL, 0}
 };

diff --git a/src/transcript_utils.c b/src/transcript_utils.c
@@ -154,14 +154,16 @@ SEXP transcript_widths(SEXP exonStarts, SEXP exonEnds)
 }
 
 SEXP tlocs2rlocs(SEXP tlocs, SEXP exonStarts, SEXP exonEnds,
-		SEXP strand, SEXP decreasing_rank_on_minus_strand)
+		SEXP strand, SEXP decreasing_rank_on_minus_strand,
+                SEXP error_if_out_of_bounds)
 {
 	SEXP ans, starts, ends, ans_elt;
-	int decreasing_rank_on_minus_strand0, ans_length,
+	int decreasing_rank_on_minus_strand0, oob_error, ans_length,
 	    i, transcript_width, on_minus_strand, nlocs, j, tloc;
 
 	decreasing_rank_on_minus_strand0 =
 		LOGICAL(decreasing_rank_on_minus_strand)[0];
+	oob_error = LOGICAL(error_if_out_of_bounds)[0];
 	ans_length = LENGTH(tlocs);
 	PROTECT(ans = duplicate(tlocs));
 	for (i = 0; i < ans_length; i++) {
@@ -191,11 +193,18 @@ SEXP tlocs2rlocs(SEXP tlocs, SEXP exonStarts, SEXP exonEnds,
 			if (tloc == NA_INTEGER)
 				continue;
 			if (tloc < 1 || tloc > transcript_width) {
-				UNPROTECT(1);
-				error("'tlocs[[%d]]' contains \"out of limits\" "
-				      "transcript locations (length of "
-				      "transcript is %d)", j + 1, transcript_width);
-			}
+                                if (oob_error) {
+				        UNPROTECT(1);
+				        error("'tlocs[[%d]]' contains "
+                                              "\"out of limits\" transcript "
+                                              "locations (length of "
+				              "transcript is %d)", j + 1, 
+                                        transcript_width);
+				} else {
+			                INTEGER(ans_elt)[j] = NA_INTEGER;
+                                        break;
+                                }
+                        }
 			INTEGER(ans_elt)[j] = tloc2rloc(tloc,
 				starts, ends,
 				on_minus_strand,