fixing possible exception when reading SCF files

occurs when reading SCF files without comments or private data Signed-off-by: Hannes Brandstätter-Müller <hannes.mueller@gmail.com>
biojava · Apr 19, 2013 · 4a95213970c3974cd1046d97aacad325ea5636f4 · 4a95213
1 parent aa4aa0b
commit 4a95213970c3974cd1046d97aacad325ea5636f4
Unified Split

Showing with 6 additions and 2 deletions.

+6 −2 sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java
diff --git a/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java b/sequencing/src/main/java/org/biojava/bio/program/scf/SCF.java
@@ -361,8 +361,12 @@ public void parse() throws IOException,
            TreeMap sectionOrder = new TreeMap();
            sectionOrder.put(new Long(header.samples_offset),  SAMPLES);
            sectionOrder.put(new Long(header.bases_offset),    BASES);
-            sectionOrder.put(new Long(header.comments_offset), COMMENTS);
-            sectionOrder.put(new Long(header.private_offset),  PRIVATE);
+            if (header.comments_size > 0) {
+                sectionOrder.put(new Long(header.comments_offset), COMMENTS);
+            }
+            if (header.private_size > 0) {
+                sectionOrder.put(new Long(header.private_offset), PRIVATE);
+            }
            
            for (Iterator it = sectionOrder.keySet().iterator() ;
            it.hasNext() ;) {