Browse code

stream past XS counts for indels (even when XS counting is disabled)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@113152 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 01/02/2016 20:11:05
Showing2 changed files

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@@ -9,7 +9,7 @@ Description: GSNAP and GMAP are a pair of tools to align short-read
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         methods to work with GMAP and GSNAP from within R. In addition,
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         it provides methods to tally alignment results on a
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         per-nucleotide basis using the bam_tally tool.
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-Version: 1.13.9
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+Version: 1.13.10
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 Depends: R (>= 2.15.0), methods, GenomeInfoDb (>= 1.1.3),
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         GenomicRanges (>= 1.17.12)
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 Imports: S4Vectors (>= 0.9.25), IRanges, Rsamtools (>= 1.17.8),
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@@ -195,19 +195,20 @@ read_xs_counts(unsigned char **bytes, int row, int *count_xs_plus,
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                int *count_xs_minus)
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 {
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     int n_xs = read_int(bytes);
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-    if (count_xs_plus == NULL) {
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-        return;
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+    if (count_xs_plus != NULL) {
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+        count_xs_plus[row] = 0;
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+        count_xs_minus[row] = 0;        
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     }
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-    count_xs_plus[row] = 0;
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-    count_xs_minus[row] = 0;
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     for (int index = 0; index < n_xs; index++) {
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 	int xs = read_int(bytes);
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 	int count = read_int(bytes);
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-	if (xs == 1) {
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-	    count_xs_plus[row] = count;
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-	} else if (xs == 2) {
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-	    count_xs_minus[row] = count;
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-	} 
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+        if (count_xs_plus != NULL) {
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+            if (xs == 1) {
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+                count_xs_plus[row] = count;
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+            } else if (xs == 2) {
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+                count_xs_minus[row] = count;
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+            }
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+        }
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     }
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 }
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